Biology subjects

Kim, H.

Publications and source records attributed to Kim, H..

At least 145 records · Page 8Linked to original sources

bioRxiv2025

Transport of sphingolipids by yeast Npc2 supports phase separation of the vacuole membrane

The yeast vacuole membrane forms ordered microdomains that facilitate micro-lipophagy under nutrient limitation. We previously found that this process involves the intracellular sorting of sphingolipids to the vacuole. While multiple vacuole protein pathways have been identified, corresponding mechanisms for lipid sorting remain undefined. Here we use a range of approaches to identify how endocytic sorting and intraluminal transport of sphingolipids contribute to the formation of vacuole domains. To visualize sphingolipid trafficking, we employed the ceramide analogue BODIPY C12-ceramide (BODIPY-Cer), which is internalized by cells and stains the vacuole. We observed that cells lacking Vps29 and Vps30, proteins involved in endosomal sorting, show altered vacuole domains and accumulate BODIPY-Cer at sites proximal to the plasma membrane. Subsequent incorporation of endocytic-derived ceramide into the vacuole is dependent on the Niemann-Pick Type C 2 protein (Npc2). Loss of Npc2 reduces domain formation and causes BODIPY-Cer to accumulate within the vacuole lumen. Both intra-vacuole trafficking of BODIPY-Cer and membrane phase separation were not dependent on Npc2s canonical receptor, Ncr1. Lipidomics of isolated vacuoles confirmed that Npc2 independently mediates sphingolipid sorting under micro-lipophagy conditions. In liposome assays, Npc2 robustly transports analogues of ceramide and inositol phosphorylceramide, a complex sphingolipid that is enriched in phase-separated vacuoles. We propose that the enlarged binding cavity of yeast Npc2 is specialized for the incorporation of sphingolipids into the vacuole membrane.

biochemistry↗

bioRxiv2025

Site-specific replacement of large-scale DNA fragments in human cells

Despite advances in genome editing1-4, precisely replacing large-scale fragments in human cells remains a significant challenge. Here, we present a site-specific gene replacement tool, named Prime Assembly (PA), which adapts prime editors to produce one or two pairs of 3-flaps on both the genome and donor plasmids. These 3-flaps anneal to each other precisely, similar to "Gibson Assembly" in DNA oligonucleotides5, allowing megabase-scale genomic excision and/or kilobase-scale donor insertion at the gene of interest. The PA system achieves an efficiency of up to 57.8% in replacing endogenous sequences with a 2.9 kbp donor DNA fragment in HEK293T cells, and presents an accuracy of more than 99% for integrated PA fragments. Ultimately, the site-specific replacement of large-scale coding sequences (CDSs) in disease-related genes can restore gene function across numerous patients with different mutations, providing a gene implantation technique for genome editing and a universal therapeutic approach.

molecular biology↗

bioRxiv2025

Biomarker Discovery via Integrative Multi-omics for Children exposed to Humidifier Disinfectant

RationaleExposure to humidifier disinfectants has been linked to an array of pulmonary disorders and diminished lung functionality particularly reduced Forced Vital Capacity (FVC). ObjectivesThis investigation sought to identify diagnostic biomarkers for early detection of children at elevated risk of developing chronic respiratory conditions following such exposure. MethodsOur research employed a comprehensive multi-omics strategy analyzing 70 pediatric patients alongside 10 controls, seamlessly integrating clinical assessments with transcriptomics, methylomics, proteomics, and metabolomics data. The analytical framework utilized a sophisticated combination of Non-negative Matrix Factorization (NMF), Multi-Omics Factor Analysis (MOFA), and advanced machine learning algorithms. Measurements and Main ResultsNMF clustering uncovered distinctive protein expression patterns associated with integrin-mediated signaling pathways and immune response mechanisms. Complementarily, MOFA identified latent factors correlating with lung function metrics, highlighting critical molecular pathways involved in integrin cell surface interactions and lipid metabolism regulation. Machine learning-based analysis facilitated the development of a multi-marker panel-comprising IGHV2-70, LysoPC (16:0), and hexadecyl ferulate-which achieved 81.46% accuracy in identifying pulmonary dysfunction cohort. ConclusionsThese findings suggest that alterations in integrin-related signaling networks and dysregulation of lipid metabolism play pivotal roles in mediating the long-term pulmonary consequences of humidifier disinfectant exposure. The proposed multi-marker panel offers significant potential for enhanced risk stratification and timely therapeutic intervention. At a Glance CommentaryO_ST_ABSScientific Knowledge on the SubjectC_ST_ABSExtensive epidemiological evidence has established the causal relationship between humidifier disinfectant exposure and pulmonary dysfunction; however, clinically validated biomarkers for predicting chronic lung disease progression remain limited. Pediatric populations demonstrate unique pathophysiological mechanisms distinct from adults, highlighting the critical necessity for biomarker identification grounded in comprehensive molecular understanding. Despite advances in omics technologies, recent investigations have encountered significant obstacles in achieving deeper mechanistic insights, predominantly attributable to methodological constraints in harmonizing clinical phenotypes with high-dimensional molecular datasets. What This Study Adds to the FieldThis investigation elucidates the fundamental contributions of integrin-mediated signaling cascades and lipid metabolic networks to persistent pulmonary dysfunction following humidifier disinfectant exposure. Our analyses revealed coordinated regulation of integrin signaling pathways and immune response networks through NMF clustering, indicating dynamic temporal evolution of inflammatory responses during chronic disease progression, with temporally distinct molecular signatures identified across discrete observation intervals. Multi-omics factor analysis (MOFA) corroborated integrin pathway dysregulation while additionally uncovering systematic suppression of lipid metabolic processes. Furthermore, machine learning algorithms enabled development of a robust three-component biomarker panel--encompassing IGHV2-70, LysoPC (16:0), and hexadecyl ferulate--demonstrating 81.46% classification accuracy for pulmonary dysfunction phenotypes. Collectively, these findings substantially advance mechanistic understanding of chronic lung injury in vulnerable pediatric cohorts and identify clinically relevant biomarkers with translational potential for risk stratification and therapeutic targeting in clinical practice.

systems biology↗

bioRxiv2025

Proteomic Signatures of Hepatitis B Virus Mutations Reveal Genotype-Specific Host Responses and Biomarker Candidates

Hepatitis B virus (HBV) remains a global health challenge, with viral genetic heterogeneity and mutation-driven resistance complicating treatment outcomes. While previous genomic and transcriptomic studies have characterized HBV mutations, the proteomic consequences of these variants remain underexplored. In this study, we applied liquid chromatography- mass spectrometry (LC-MS)-based proteomics and systems biology approaches to serum samples from 60 HBV-infected patients, stratified by mutation-defined genotype signatures. Four genotype groups were generated, including those harboring mutation related to liver disease progression (rt269/s184) and basal core promoter/precore mutations (A1762T/G1896A). Comparative analyses of 406 high-abundance plasma proteins revealed distinct proteomic signatures, particularly in the ##AG group lacking mutation related to liver disease progression motifs. This group exhibited elevated CRISPLD2 and HSPD1 expression, implicating a dual axis of anti-inflammatory buffering and chaperone-mediated viral processes. Network and co-expression analyses identified modules enriched in focal adhesion, extracellular matrix remodeling, angiogenesis, and PI3K/Akt signaling--pathways tightly linked to hepatocarcinogenesis. Protein-protein interaction enrichment further highlighted disruption of chaperone networks, cytoskeletal regulation, and unfolded protein response. These findings provide molecular evidence for genotype-specific host-virus interactions, nominate CRISPLD2 and HSPD1 as biomarker candidates, and suggest therapeutic strategies targeting PI3K/Akt and microenvironmental pathways. Our results underscore the value of proteomics in refining genotype-informed risk stratification and personalized management in chronic HBV.

systems biology↗

bioRxiv2025

Human-specific features of the cerebellum and ZP2-regulated synapse development

Understanding the unique features of the human brain compared to non-human primates has long intrigued humankind. The cerebellum refines motor coordination and cognitive functions, contributing to the evolutionary development of human adaptability and dexterity. To identify shared and divergent features across primates, we conducted single-nucleus transcriptomic and chromatin accessibility profiling of the adult cerebellar cortex in humans, chimpanzees, macaques, and marmosets. We revealed human-specific transcriptomic and regulatory features, particularly those involved in synaptogenesis. Notably, we identified an enrichment of the sperm receptor zona pellucida glycoprotein 2 (ZP2) and its potential interactors, known for their roles in gamete interaction, in human granule cells. Experimental data show that ZP2 expression in human granule cells is induced by pontine mossy fibers, reducing synaptic proteins at pontocerebellar glomerular synapses, and decreasing cerebellar neuron electrophysiological activity. This unexpected co-option of ZP2 in human-specific synapse regulation provides insights into the evolutionary specialization of the human cerebellum.

neuroscience↗

bioRxiv2025

Empirical optimization of dual-sgRNA design for in vivo CRISPR/Cas9-mediated exon deletion in mice

CRISPR/Cas9 has transformed gene editing, enabling precise genetic modifications across species. However, existing sgRNA design prediction models based on in vitro data are difficult to generalize to in vivo contexts. In particular, approaches based on single-sgRNA design require additional filtering of in-frame mutations, which is inefficient in terms of both time and cost. In this study, we developed the first mammalian in vivo-trained prediction model to evaluate the efficiency of a dual-sgRNA-based exon deletion strategy. Using 230 editing outcomes of postnatal viable individuals, eight prediction models were constructed and evaluated based on generalized linear models and random forests. The final selected model, a Combined GLM, integrated the DeepSpCas9 score with k-mer sequence features, achieving an AUC of 0.759 (95% Confidence Interval: 0.697-0.821). Motif analysis revealed that CC sequences were associated with high efficiency and TT sequences were associated with low editing efficiency. This study demonstrates that integrating sequence-based features with existing design scores can improve sgRNA efficiency prediction in vivo. The proposed framework can be applied to the development of next-generation sgRNA design tools, with direct implications for gene therapy, effective animal model generation, and precision genome engineering. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/675005v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@12e6170org.highwire.dtl.DTLVardef@1ff2599org.highwire.dtl.DTLVardef@1fd61dborg.highwire.dtl.DTLVardef@23a426_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

DART: A GUI Pipeline for Aligning Histological Brain Sections to 3D Atlases and Automating Laser Microdissection

The precise dissection of anatomically defined brain regions is the basis of many workflows in neurobiology. Traditionally, brain regions of interest are defined by visual inspection of tissue sections, followed by manual dissection. Recently, laser capture microscopes have been employed for more accurate dissection, but region identification is still challenging. This paper presents an open-source software pipeline DART (Dissecting Atlas-Registered Tissue) that aligns histological brain sections to three-dimensional reference atlases and exports the resulting region-of-interest (ROI) contours for dissection by Leica Laser Microdissection (LMD) instruments. By integrating well-established image-processing libraries with a user-friendly graphical user interface, the software automates the traditionally time-consuming workflow of defining the boundaries of brain regions for dissection. With this pipeline, researchers can streamline tissue sampling for molecular analyses, while ensuring reproducibility and precision in ROI selection.

bioengineering↗

bioRxiv2025

BOGO: A Proteome-Wide Gene Overexpression Platform for Discovering Rational Cancer Combination Therapies

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/673780v2_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@19d5d7dorg.highwire.dtl.DTLVardef@64f7eborg.highwire.dtl.DTLVardef@d08b75org.highwire.dtl.DTLVardef@173c448_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG Cancer drug resistance remains a major barrier to durable treatment success, often leading to relapse despite advances in precision oncology. While combination therapies are being increasingly investigated, such as chemotherapy with small molecule inhibitors, predicting drug response and identifying rational drug combinations based on resistance mechanisms remain major challenges. Therefore, a proteome-wide, single-gene overexpression screening platform is essential for guiding rational therapy selection. Here, we present BOGO (Bxb1-landing pad human ORFeome-integrated system for a proteome-wide Gene Overexpression), a robust, scalable, and reproducible screening platform that enables single-copy, site-specific integration and overexpression of [~]19,000 human open across cancer cell models. Using BOGO, we identified drug-specific response drivers for 16 chemotherapeutic agents and integrated clinical datasets to uncover proliferation and resistance-associated genes with prognostic potential. Drug response similarity networks revealed both shared and unique mechanisms, highlighting key pathways such as autophagy, apoptosis, and Wnt signaling, and notable resistance-associated genes including BCL2, POLD2, and TRADD. In particular, we proposed a synergistic combination of the BCL2 family inhibitor ABT-263 (Navitoclax(R)) and the DNA analog TAS-102 (Lonsurf(R)), which revealed that lysosomal modulation is a key mechanism driving DNA analog resistance. This combination therapy selectively enhanced cytotoxicity in colorectal and pancreatic cancer cells in vitro, and demonstrated therapeutic benefit in vivo in both cell line-derived xenograft (CDX) and patient-derived xenograft (PDX) models. Together, these findings establish BOGO as a powerful gene overexpression perturbation platform for systematically identifying chemoresistance and chemosensitization drivers, and for discovering rational combination therapies. Its scalability and reproducibility position BOGO as a broadly applicable tool for functional genomics and therapeutic discovery beyond cancer resistance.

systems biology↗

bioRxiv2025

In Silico Design of APOE ε4 Interaction Inhibitor Peptides for Alzheimer's Disease

BackgroundProtein-protein interactions (PPIs) are essential for cellular functions, and their aberrant formation contributes to neurodegenerative diseases. Alzheimers disease (AD), characterized by its complex pathogenesis, poses an increasing societal burden with population aging. The APOE {varepsilon}4 allele represents the strongest genetic risk factor for late-onset AD, yet its pathological mechanisms remain incompletely understood. MethodsWe employed artificial intelligence-driven peptide design to elucidate the pathological interaction between APOE {varepsilon}4 and amyloid precursor protein (APP). Using advanced AI algorithms, we identified critical binding interfaces and designed mimetic peptides targeting the APOE {varepsilon}4-APP interaction site. Peptide efficacy was evaluated through comprehensive molecular dynamics simulations. ResultsOur analysis revealed key residues mediating APOE {varepsilon}4-APP binding. The designed inhibitory peptides demonstrated stable interaction with target sites, favorable binding energetics, and sustained structural integrity throughout simulations. Lead candidate effectively disrupted APOE {varepsilon}4- APP complex formation in silico. ConclusionThis study presents a novel AI-powered approach for developing PPI-targeted therapeutics against AD. Our computationally validated peptide inhibitors offer promising therapeutic candidates that warrant experimental validation. These findings demonstrate the potential of integrating artificial intelligence with structural biology for accelerating drug discovery in neurodegenerative diseases.

bioinformatics↗

bioRxiv2025

An integrated in silico-in vitro workflow for discovering high-affinity, selective antibodies to the KRAS(G12D)-MHC I complex

Antibodies that recognize peptide-loaded class I major histocompatibility complex (pMHC I) molecules could enable therapeutic targeting of intracellular oncogenic proteins, yet their discovery has been hampered by the small size of peptide antigens and allele-specificity. We describe an integrated in silico-in vitro workflow for generating high-affinity, selective antibodies to KRAS(G12D)10 presented by HLA-C*08:02, a clinically validated cancer neoantigen. In silico, multiple human antibody-derived variable fragments (Fvs) plausibly docked to the target pMHC were generated, followed by limited complementarity-determining region (CDR) sequence design. In vitro, CDR diversity was introduced at 3-4 positions per Fv to construct yeast surface display library for iterative selections. This workflow yielded antibodies with exclusive binding to KRAS(G12D)10/HLA-C*08:02 without cross-reactivity. Affinity maturation achieved nanomolar dissociation constants, and incorporation into chimeric antigen receptor T cells enabled specific activation against target-positive cells. This study establishes a practical design-to-function pipeline for TCR-like antibody discovery, and demonstrates the feasibility of therapeutic targeting against KRAS(G12D)-driven malignancies.

biochemistry↗

bioRxiv2025

Platelet factor 4 modulates endothelial cell antimicrobial activity to enhance bacterial clearance and improve sepsis outcomes

Sepsis is a life-threatening condition characterized by dysregulated host responses to infection. Here, we identify platelet factor 4 (PF4) as a key mediator of vascular antimicrobial defense. In vitro, PF4 enhanced endothelial cell internalization of Escherichia coli via interactions with the PF4 receptor CXCR3 and the endothelial glycocalyx, directing bacteria to clathrin-mediated endocytosis and lysosomal degradation. In vivo, PF4 administration improved survival and reduced sepsis severity, bacterial burden, inflammation, and thrombosis in wild-type (WT) and PF4 knockout (PF4-/-) mice challenged with systemic polymicrobial infection. Using intravital microscopy, we observed that infused bacteria were rapidly sequestered in the pulmonary microvasculature. However, PF4-/- mice exhibited impaired bacterial clearance and increased microvascular platelet adhesion and aggregation. In the liver, following Kupffer cell depletion, PF4-/- mice had increased sinusoidal platelet accumulation, larger bacterial aggregates, and elevated hepatic bacterial burden compared to WT controls. Collectively, these findings reveal that PF4 promotes bacterial clearance and restrains immunothrombosis during sepsis in part via endothelial cell uptake and destruction of microbes. By enhancing endothelial antimicrobial function, PF4 represents a significant yet previously underrecognized host defense mechanism that limits bacterial spread and alleviates vascular injury during infection. KEY POINTSO_LIIn vitro, PF4 accelerates bacterial clearance by enhancing endothelial uptake of bacteria and promoting their trafficking to the lysosome. C_LIO_LIIn murine sepsis, PF4 augments pathogen clearance to reduce infection severity, limit organ injury, and improve survival. C_LI

cell biology↗

bioRxiv2025

Integrative Analysis of Proteomics and Metabolomics Reveals Impacts of Sam2 Knockout on Autism Spectrum Disorders

Neurokine Sam2 deficiency is associated with behavioral abnormalities including heightened anxiety and fear responses across evolutionarily conserved model organisms. Here, we employed an integrated proteomics and metabolomics approach using liquid chromatography-mass spectrometry (LC-MS) to elucidate molecular signatures associated with autism spectrum disorder (ASD) in Sam2 knockout mice. Comparative analysis of blood plasma samples from Sam2 knockout and wild-type mice revealed substantial alterations in both proteomic and metabolomic profiles. Proteomic analysis identified 68 differentially expressed proteins (comprising 102 peptides), with notable upregulation of complement component C1qc and downregulation of apolipoprotein A1 (Apoa1), implicating dysregulation of complement cascade pathways. Metabolomic profiling uncovered 15 significantly altered metabolites: nine upregulated species including D-glucuronic acid and 5,10-Methylenetetrahydrofolate, and six downregulated metabolites including folinic acid and acetate. Integrative pathway analysis revealed perturbations in glycolysis/gluconeogenesis and glycerophospholipid metabolism, providing mechanistic insights into the molecular consequences of Sam2 deficiency. These findings identify potential biomarkers for anxiety-related disorders and ASD while advancing our understanding of the complex interplay between genetic alterations and proteomic-metabolomic networks in neurodevelopmental conditions. Our results establish a foundation for developing targeted therapeutic interventions and highlight the utility of multi-omics approaches in dissecting the molecular basis of behavioral disorders.

systems biology↗

bioRxiv2025

Rejuvenation-Responsive and Senolytic-Sensitive Muscle Stem Cells Unveiled by CD200 and CD63 in Geriatric Muscle

Muscle stem cells (MuSCs) are parenchymal cells in skeletal muscle regeneration and maintenance. With aging, MuSCs experience a decline in their regenerative function and reduction in their number. However, recent evidence points to substantial heterogeneity within the aged MuSC population, raising questions about the underlying mechanisms of age-associated dysfunction. Here, we used Pax7CreERT2;RosaYFP mice (MuSCYFP) to label Pax7-expressing MuSCs and chronologically traced MuSCs until geriatric age. Genetic labeling and chronological tracing revealed that the number of YFP+ MuSC remained comparable between young, middle and geriatric ages. At geriatric age, YFP+ MuSCs exhibited reduced expression of traditional MuSC markers such as VCAM1 and PAX7. A previously unrecognized subpopulation emerged, characterized by loss of VCAM1 and low or absent PAX7. Despite their altered marker profile, these cells retained transcriptional signatures of quiescence and myogenic potential, but displayed significantly reduced proliferative and regenerative capacities. They displayed gene expression patterns indicative of senescence-like state and were selectively ablated by senolytic treatment. DHT restored regenerative function in aged mice and re-induced VCAM1 expression in YFP+/Pax7-/low/VCAM1- cells, indicating responsiveness to rejuvenation. Based on their emergence with aging, functional impairment and responsiveness to rejuvenation, we termed this population GERI-MuSCs (Geriatric Emerging Rejuvenation-responsive and Impaired MuSCs). CD63 and CD200 were identified as novel surface markers that together with VCAM1, reliably detect GERI-MuSCs as well as classical Pax7+/VCAM1High MuSCs, providing a tool for comprehensive isolation of MuSCs from aged wild-type mice. Together, our findings provide a refined framework for studying MuSC aging and offer new tools for isolating functionally distinct MuSC subsets from aged skeletal muscle.

developmental biology↗

bioRxiv2025

Interstitial macrophages prevent tuberculosis relapse by restricting Mycobacterium tuberculosis immune evasion

Alveolar macrophages (AMs) are the first immune cells to encounter Mycobacterium tuberculosis (Mtb) in the lungs, but they frequently fail to eliminate this causative agent of tuberculosis (TB), allowing Mtb to persist or replicate. Interstitial macrophages (IMs) are recruited to restrict Mtb growth and limit immune evasion. While IMs have been implicated in the control of acute Mtb infection, their role during latent tuberculosis infection (LTBI) has not yet been explored. We hypothesized that IMs contribute to maintaining latency and that their depletion during LTBI would promote Mtb reactivation, leading to TB relapse and disease. To test this, we utilized our previously established mouse model of paucibacillary Mtb infection that mimics aspects of LTBI in humans to selectively deplete IMs during the latent phase. IM depletion led to TB relapse in 26% of mice compared to 2% in control mice. The transitory depletion of this macrophage subset transiently affected both pulmonary macrophage and neutrophil populations. Mice that relapsed exhibited an increased proportion of pro-inflammatory IMs and elevated concentrations of G-CSF, GM-CSF, IL3, IL-12, IL-13, IL-17A and KC in the lung. These findings indicate that IMs play a critical role in controlling latent Mtb and preventing TB relapse.

immunology↗

bioRxiv2025

Topological spatial coding for rapid generalization in the hippocampal formation

The brain navigates complex environments by combining entorhinal grid codes with hippocampal place codes. Although grid codes effectively represent a current environments geometry, their capacity to generalize across topologically analogous environments with different reward and state structures remains poorly understood. We introduce topology-aware grid coding (TAG), a computational theory that leverages topological invariance to generalize to new environments with the same topological structure but with different geometry. Drawing on the Euler characteristic from algebraic topology, TAG integrates complementary neural codes built on foundational grid bases: place codes serving as 0D vertices for self-localization, boundary codes acting as 1D edges to learn policy-independent grid codes through state prediction errors, and corner codes functioning as 2D faces for identifying topologically significant states. TAG grid codes remain stable under topology-preserving deformations yet discriminate among non-isomorphic structures. TAG develops policy-independent grid codes for novel structures more rapidly and robustly than existing approaches, balancing structure and policy encoding for multi-subgoal navigation without extensive planning. Finally, we show that TAG is compatible with transformer architectures, enabling its integration into scalable neural networks. Together, the TAG theory describes the essential nature of geometric objects to explain how the entorhinal-hippocampal system maps the unique topological structure of spaces.

neuroscience↗

bioRxiv2025

Filomicelle-Embedded Composite Hydrogels for Localized Gelation within the Anterior Chamber of the Eye

Nanocarriers hold transformative potential for treating anterior segment eye diseases, yet corneal epithelium impermeability necessitates intraocular injection. Given the discomfort and infection risk, an injectable hydrogel-based depot offers a promising strategy for sustained nanocarrier delivery in intraocular therapy. However, because the aqueous humor is a large, fluid-filled environment, achieving spatially confined gelation remains a key challenge as injected materials rapidly diffuse. Herein, we present a composite hydrogel (C-gel) that enables localized in situ gelation and sustained nanocarrier release within the anterior chamber. This is achieved using poly(ethylene glycol)-b-poly(propylene sulfide) (PEG-b-PPS) filomicelles (FMs), whose filamentous structure confines crosslinking reactions spatially, promoting efficient gel formation. As a result, 90% of the injected polymer is retained within the crosslinked hydrogel matrix. Embedded FMs then undergo oxidation-induced cylinder-to-sphere transitions, facilitating gradual release of micellar nanocarriers. The rheological properties, gelation timing, and microstructure of the C-gel are adjustable, allowing precise control of nanocarrier release dynamics. In vivo evaluation in mice confirmed excellent biocompatibility without inducing intraocular pressure elevation, ocular toxicity, or immune cell infiltration. Sustained release of nanocarriers was observed for over a month under conditions mimicking that of the anterior chamber of the eye, underscoring the potential of C-gels for long-term drug delivery in anterior segment eye diseases therapy.

bioengineering↗

bioRxiv2025

Linking Kinetochore Attachment to Checkpoint Control: The Role of Aurora B in BubR1 Acetylation

We report here that Aurora B kinase is critical in BubR1 acetylation at K250, transducing kinetochore attachment status to spindle assembly checkpoint (SAC) activity. Aurora B phosphorylates BubR1 at serines 16 and 39 in an unattachment-dependent manner, which is a prerequisite for BubR1 acetylation at lysine 250 (K250). Utilizing a novel anti-AcK250 monoclonal antibody in structured illumination microscopy (SIM), we reveal that BubR1 acetylation is associated with kinetochore expansion, evidenced by crescent-shaped volume increase of ZW10 and Mad2 surrounding the kinetochore. Furthermore, K250-BubR1 acetylation enhances its interaction with CENP-E, a kinesin crucial for chromosome alignment through facilitating end-on attachment. Disrupting Aurora B-mediated phosphorylation of Ser16/39 impaired K250 acetylation, compromising both fibrous corona polymerization and mitotic checkpoint complex (MCC) maintenance. Conversely, introducing K250 acetylation mimetic form rescued MCC and fibrous corona in cells expressing phosphorylation-deficient S16A/S39A mutants. Our findings reveal Aurora B-BubR1 acetylation axis as a critical SAC signaling pathway, interlinking unattachment sensing with kinetochore expansion and SAC activity. We propose that this stepwise phosphorylation-acetylation on BubR1 constitutes a crucial part of SAC signaling code, transducing unattachment signal to fibrous corona polymerization and SAC activity. This phosphorylation-acetylation cascade in BubR1 offers potential therapeutic targets in treating cancers of chromosome instability.

cell biology↗

bioRxiv2025

The Data Distillery: A Graph Framework for Semantic Integration and Querying of Biomedical Data

The Data Distillery Knowledge Graph (DDKG) is a framework for semantic integration and querying of biomedical data across domains. Built for the NIH Common Fund Data Ecosystem, it supports translational research by linking clinical and experimental datasets in a unified graph model. Clinical standards such as ICD-10, SNOMED, and DrugBank are integrated through UMLS, while genomics and basic science data are structured using ontologies and standards such as HPO, GENCODE, Ensembl, STRING, and ClinVar. The DDKG uses a property graph architecture based on the UBKG infrastructure and supports ontology-based ingestion, identifier normalization, and graph-native querying. The system is modular and can be extended with new datasets or schema modules. We demonstrate its utility for informatics queries across eight use cases, including regulatory variant analysis, tissue-specific expression, biomarker discovery, and cross-species variant prioritization. The DDKG is accessible via a public interface, a programmatic API, and downloadable builds for local use.

bioinformatics↗