Biology subjects

Ahn, J.

Publications and source records attributed to Ahn, J..

At least 19 recordsLinked to original sources

bioRxiv2026

ProteinSketch translates spatial intuition into protein design with bimanual interaction in VR

Generative AI-based protein design can create diverse structures for desired functions but offers human designers limited control over three-dimensional architectures. We developed ProteinSketch, a bimanual virtual reality platform in which immersive backbone sketches and volumetric envelopes are directly created and translated into constraints for diffusion-based protein generation. RFdiffusion-based real-time refinement enabled interactive exploration and construction of user-specified protein topologies. Volumetric conditioning of sketched envelopes enabled high-fidelity control of anisometric geometries, confirmed by cryo-electron microscopy. These user-defined volumetric constraints enabled functional-binder design and extension of pre-existing minibinders to surfaces otherwise difficult to access within complex molecular environments using conventional design approaches. This collaborative human-AI framework integrates human spatial reasoning with generative AI for spatially directed, shape-controlled design of protein structure and function. One-sentence summaryImmersive ProteinSketch embeds human spatial reasoning in AI-guided design of protein topology, shape, and function.

bioengineering↗

bioRxiv2026

Development of an Exploratory Taxonomy for Veterinary Professionals' AI Query Patterns Across Clinical Stages: An Expert Panel Study

Background/ObjectivesThe integration of large language model (LLM)-based AI tools into veterinary clinical practice is rapidly increasing; however, no systematically derived taxonomy of veterinary AI query patterns has been established. This study aimed to develop and refine an exploratory taxonomy of veterinary AI query patterns across clinical stages through a structured expert-panel review process. MethodsAn exploratory cross-sectional expert panel study was conducted. 5,372 real-world query logs from a veterinary clinical AI chatbot deployed over eight months were analyzed using AI-assisted inductive coding to derive an initial taxonomy. The taxonomy was refined through literature review and subsequently reviewed by an expert panel of 38 veterinary professionals via structured online survey across five clinical stages. ResultsA taxonomy of 3 categories and 21 subtypes was established: Clinical Support Queries (Types A-H), Evidence-Based Research Queries (Types I-L), and Terminology and Drug Reference Queries (Types M-U). Type B (Differential Reasoning) had the highest overall frequency (57/188 first-choice responses), while Type D (Clinical Decision Support) was dominant immediately post-consultation (55.3%). Veterinary professionals with [≥]10 years of experience showed a higher frequency of Type G (Evidence Search) preference than those with <10 years of experience (18 vs. 4), while university-affiliated professionals demonstrated a distinct pattern dominated by Type G. ConclusionsTo our knowledge, no published study has previously established a veterinary-specific, clinical-stage-sensitive exploratory taxonomy of AI query patterns; this study addresses that gap. The findings provide a foundational framework for designing context-aware, stage-adaptive veterinary AI systems and benchmark evaluation tools.

scientific communication and education↗

bioRxiv2026

Structural Basis for Inhibition of the HKU5-CoV Main Protease by Clinical SARS-CoV-2 Protease Inhibitors

The identification of Pipistrellus bat coronavirus HKU5 lineage 2 (HKU5-CoV-2) as a human ACE2-adapted virus highlights the need for antiviral strategies to control emerging HKU5-related merbecoviruses. However, despite the importance of the main protease (Mpro) as a key antiviral target, structural and biochemical characterization of HKU5-CoV Mpro in the context of clinical inhibitors has remained limited. Here, we obtained high-resolution crystal structures of HKU5-CoV-1 Mpro in its apo state (1.75 [A]) and in complex with the approved covalent inhibitor nirmatrelvir (1.91 [A]) and the non-covalent inhibitor ensitrelvir (1.55 [A]). These structures reveal an induced-fit mechanism, in which the S2 loop containing Met49 adopts an open conformation in the apo state and undergoes inhibitor-specific conformational changes upon nirmatrelvir and ensitrelvir binding. These structures served as a foundation for the characterization of HKU5-CoV-2 Mpro via modeling and molecular dynamics simulations. Biochemical assays revealed that HKU5-CoV-1 and HKU5-CoV-2 Mpro exhibited nearly identical kinetic profiles, with turnover rates approximately two-fold higher than SARS-CoV-2 Mpro. Structural analysis revealed a highly conserved S1 subsite but distinct local environments in the S1', S2, and S4 substrate-binding sites relevant to inhibitor recognition. Despite these variations, nirmatrelvir and ensitrelvir showed potent inhibitory activity, with comparable double-digit nanomolar IC50 values across all three Mpro proteins. Computational analyses indicated that HKU5-CoV-2 Mpro engages nirmatrelvir and ensitrelvir in binding modes comparable to those observed for HKU5-CoV-1, supporting a conserved mechanism of inhibitor recognition and providing a structural basis for developing pan-coronavirus antivirals targeting emerging merbecoviruses.

biochemistry↗

bioRxiv2026

Long-Lasting Electrohydrodynamically Printed Transparent Soft Microelectrode for Implantable Biointerfaces

Reliable and scalable soft implantable neural interface fabrication remains a key challenge for chronic bioelectronic applications. Here, we present a transparent soft microelectrode fabricated with electrohydrodynamic (EHD) printing, utilizing the fluorinated polymer poly(vinylidene fluoride-co-hexafluoropropylene) (PVDF-HFP) and poly (3, 4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT: PSS) to form seamless, selectively patterned multilayer structures with low impedance and long-term stability. Controlled in situ curing during printing yields dense, void-free substrate and encapsulation layers, suppressing interfacial defects and ionic pathways, while maintaining high optical transparency (>60%) with PEDOT:PSS. The printed microelectrodes exhibit low impedance, high charge storage and injection capacities, and stable electrochemical behavior under biomimetic conditions. In addition, the devices demonstrate robust mechanical and electromechanical stability under cyclic deformation in both dry and wet environments, as well as under prolonged electrical stimulation. Accelerated aging studies project multi-year operational lifetimes, and in vitro/in vivo biocompatibility assessments confirm excellent tissue integration. These results establish EHD-printed fluorinated polymer-based microelectrodes as a scalable and durable platform for chronic implantable biointerfaces. ToC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=182 SRC="FIGDIR/small/726391v1_ufig1.gif" ALT="Figure 1"> View larger version (79K): org.highwire.dtl.DTLVardef@f4f717org.highwire.dtl.DTLVardef@8a34a1org.highwire.dtl.DTLVardef@185540dorg.highwire.dtl.DTLVardef@51462a_HPS_FORMAT_FIGEXP M_FIG C_FIG This report presents an electrohydrodynamically printed transparent soft microelectrode for chronic purposes. Electrohydrodynamic printing promotes seamless multilayer structures with selective deposition and long-term mechanical stability. The devices show low impedance, high charge capacity, and robust electrochemical/electromechanical properties. Accelerated aging projects [~]7.2 year lifetimes, and XPS/SEM-EDS confirm strong ion barrier properties and biocompatibility for chronic implantation.

bioengineering↗

bioRxiv2026

Rapid Peptide Mapping of Monoclonal Antibodies with Direct Infusion Mass Spectrometry

Peptide mapping is a critical tool for characterizing biotherapeutic proteins and is essential for the development of monoclonal antibody drugs. Here we describe a new direct infusion technology that streamlines peptide mapping data collection and analysis, accelerating the method by up to 100-fold. This method, which we term RaPiD-mAb-MS, combines high-throughput plate-based sample preparation with direct infusion mass spectrometry analysis. RaPiD-mAb-MS allows analysis of 96 samples within [~] 1.5 to 2 hours, routinely achieves >95% sequence coverage, and has been successfully applied to 28 unique antibodies and over 2,000 samples. Here we demonstrate that RaPiD-mAb-MS detects and quantifies oxidation, deamidation, isomerization, glycosylation, and sequence variants with results comparable to conventional LC-MS based methods in a fraction of the time. Further, by eliminating chromatography, data analysis is greatly streamlined and simplified. By allowing for the collection of [~] 1,000 peptide maps per day, RaPiD-mAb-MS is positioned to accelerate all phases of antibody-based drug discovery & development and sets the stage for collection of massive datasets that would allow artificial intelligent prediction of optimal antibody variants and formulations.

biochemistry↗

bioRxiv2026

Tuned inhibitory control of neuronal firing thresholds explains predictive sensorimotor behavior

Prior expectations guide sensorimotor behavior when sensory information is uncertain, yet the cellular mechanisms underlying this integration remain elusive. Here, we investigate how priors in sensory motion direction shape neural population dynamics by combining recurrent neural network (RNN) modeling with macaque smooth pursuit behavior and middle temporal area (area MT) electrophysiology. Our RNN model reveals that prior expectations are implemented by elevating firing thresholds in neurons tuned away from the expected direction. This selective inhibition sharpens population tuning and reduces behavioral variability under weak sensory information conditions. We validated this prediction in vivo: delta-band local field potentials in area MT, where the phase reflects neural excitability states, exhibited direction-specific phase shifts that scaled with the deviation from the expected direction. These findings demonstrate that prior expectations enhance behavioral reliability through tuned inhibitory control of neuronal excitability, providing a mechanistic link between Bayesian inference and cortical circuit dynamics.

neuroscience↗

bioRxiv2026

Tm guided exon exon junction RT-PCR enables specific detection of RNA variants lacking easily distinguishable exonic regions

Accurate detection of RNA splice variants is often hindered when transcripts lack large distinguishable exonic regions, making conventional PCR strategies challenging. We developed a simple melting temperature (Tm)-guided exon-exon junction (EEJ) RT-PCR method to enable variant-specific detection under these conditions. Uni-directional primers spanning exon-exon junctions were designed so that approximately each half anneals to adjacent exons. The Tm of each half-site was set >7{degrees}C below the annealing temperature, preventing stable binding to individual exons and enforcing junction-dependent amplification. The method was evaluated using HTRA1-AS1 long noncoding RNA variants that share overlapping exon sequences but differ in splice connectivity. HTRA1-AS1 comprises five variants, only one with a large distinguishable exon. Tm-guided EEJ primers robustly discriminated the remaining four variants. After optimization, amplification yielded sharp, single bands with minimal cross-reactivity. Compared with conventional designs, this approach reduced heteroduplex and heteroquadruplex formation, improving band clarity. Sanger sequencing confirmed junction specificity, and the method performed well in multiplex settings. Overall, Tm-guided EEJ RT-PCR is a cost-effective, high-resolution approach for detecting RNA variants lacking easily distinguishable exonic regions, readily compatible with standard RT-PCR and qPCR workflows.

molecular biology↗

bioRxiv2026

The β-lactam adjuvant guanosine potentiates anti-folate antibiotics and pyrimidine synthesis inhibitors by depleting thymidine in methicillin-resistant Staphylococcus aureus

Efforts to improve the effectiveness of existing interventions for antimicrobial-resistant (AMR) infections include identifying new ways to overcome resistance to licensed antibiotics using adjuvants or deploying antibiotics in novel combinations. Although antibiotics targeting the bacterial cell wall (e.g., {beta}-lactams) and folate metabolism (e.g., trimethoprim-sulfamethoxazole, TMP-SMX) remain cornerstones of modern healthcare, resistance to both classes poses an ongoing therapeutic challenge. We recently demonstrated that purine nucleosides can act as potent antibiotic adjuvants, restoring {beta}-lactam susceptibility in methicillin-resistant Staphylococcus aureus (MRSA). Here, we show that the {beta}-lactam adjuvant guanosine significantly reduces intracellular thymidine levels in MRSA and potentiates the activity of antifolate antibiotics (TMP-SMX) as well as the pyrimidine antimetabolites 5-fluorouracil (5-FU) and 5-fluorouridine (5-FUrd). Incorporation of oxacillin into guanosine-antifolate or guanosine-pyrimidine analogue combinations further enhanced killing of both planktonic and biofilm-associated MRSA. Thymidine depletion was accompanied by elevated intracellular reactive oxygen species (ROS) and dissipation of membrane potential, providing mechanistic insight into the bactericidal effects of these combinations. Together, these findings demonstrate that guanosine expands MRSA susceptibility beyond {beta}-lactams to include additional clinically relevant antimicrobial drug classes commonly used to treat bacterial infections. Author Summary.Finding new ways to help antibiotics to work against resistant bacteria is an important part of efforts to address the antimicrobial resistance crisis. Adjuvants, which are boosters that help antibiotics to work against resistant bacteria, are important in this regard. We recently discovered that, guanosine, which is involved in the synthesis of DNA, makes methicillin-resistant Staphylococcus aureus (MRSA) more sensitive to penicillin-type antibiotics. Here we report that guanosine also improves the effectiveness of two other types of antimicrobial drugs (anti-folate antibiotics and pyrimidine antimetabolites) that are also used in clinical practice, expanding the potential of this adjuvant to improve the management of difficult-to-treat MRSA infections.

microbiology↗

bioRxiv2026

Repeated Mild Head Injury Establishes a Senescent Cranial Bone Marrow Niche that Impairs Brain Metabolism

Traumatic brain injury (TBI) of any severity is associated with long-term systemic inflammation and increased risk of peripheral comorbidities, yet the mechanisms driving immune dysregulation and accelerated aging after repeated mild head impacts remain poorly defined. Here, we investigated the acute and chronic effects of repeated mild TBI (rmTBI) on distal and proximal bone marrow compartments in the femur and calvaria, respectively. Using a modified weight-drop mouse model delivering rotational and acceleration-deceleration forces (3 hits/week for up to 16 weeks), rmTBI produced no mortality, skull fracture, hemorrhage, or brain leukocyte infiltration. One day after three consecutive impacts, rmTBI induced robust proliferation of LSK stem/progenitor cells in both femoral and calvarial marrow, evidenced by Ki67 expression, BrdU incorporation, and increased monocyte output. By 8 weeks (24 impacts), injury-induced proliferation subsided and LSK cells exhibited increased senescence-associated {beta}-galactosidase activity and upregulation of tumor suppressor genes. At 16 weeks (48 impacts), LSK populations were depleted at both sites, displaying reduced proliferative capacity, telomere shortening, and pancytopenia in otherwise young adult mice. Calvarial bone marrow cells exposed to rmTBI released a distinct cytokine and proteomic secretome marked by elevated IL-6, suppressed mitochondrial and metabolic signaling, and enhanced DNA repair pathways. Notably, skull-derived secretome factors impaired cortical and hippocampal mitochondrial metabolism, and reduced microglial mitochondrial membrane potential. Together, these findings identify replicative senescence of the brain-adjacent bone marrow niche as an early and progressive consequence of repeated mild head injury, linking rmTBI to long-lasting metabolic dysfunction, impaired immunity, and accelerated aging. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/699107v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@683c8eorg.highwire.dtl.DTLVardef@15fc42forg.highwire.dtl.DTLVardef@48f398org.highwire.dtl.DTLVardef@170bbcc_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2026

NFATc3 enhances DREAM complex-driven tumorigenesis

The nuclear factor of activated T cells (NFAT) transcription factors, activated by calcium-calcineurin signaling, regulate various cellular processes, including cell differentiation, angiogenesis, and immune cell activation. Nonetheless, their roles in tumor cells remain largely undefined. The dimerization partner, RB-like, E2F, and multi-vulval class B (DREAM) complex orchestrates cell quiescence and proliferation. Pharmacological mimicry of DREAM-activated transcriptional signatures identified two calcium signaling inhibitors that suppressed lung adenocarcinoma (LUAD) cell proliferation. Among the five NFAT members, NFATc3/NFAT4 was predominantly expressed in LUAD cells and required for both LUAD cell proliferation and DREAM target gene transactivation. NFATc3 was enriched at DREAM target promoters and associated with the DREAM complex, possibly via LIN9, a scaffolding protein of the Multi-Vulva class B (MuvB) core proteins. These findings reveal an unexpected role for NFATc3 in promoting DREAM target gene transactivation and suggest the calcium-NFATc3 axis as a molecular target in LUAD, enriched by DREAM complex activation.

molecular biology↗

bioRxiv2026

A novel imprinting cluster at the porcine CRSP complex locus defines a species-specific imprinted domain

BackgroundGenomic imprinting is an epigenetic phenomenon that results in parent-of-origin-specific gene expression and has been extensively characterized in mice and humans. However, in pigs, imprinting has been investigated primarily through analyses of orthologs of known imprinted genes in mice and humans. The objective of this study was to examine DNA methylation status and gene expression at a porcine locus containing newly identified imprinted calcitonin receptor-stimulating peptide (CRSP)-encoding genes, to compare orthologous loci in mice and humans, and to investigate a potential underlying mechanism. ResultsAnalyses of differentially methylated regions (DMRs) between porcine parthenogenetic embryos and biparental controls revealed multiple parental DMRs at a locus we term the CRSP complex locus, which harbors CRSP-encoding genes that likely arose through gene duplication. In contrast, orthologous genomic intervals in mice and humans exhibited unmethylated promoters and lacked evidence of imprinting. Consistently, CRSP-encoding genes in pigs showed parent-of-origin-specific monoallelic expression, whereas genes within the orthologous locus in mice and humans were biallelically expressed. Further analysis indicated that porcine CRSP promoters are embedded within oocyte-expressed alternative transcripts and co-occurred with DNA methylation, suggesting a transcription-dependent imprinting mechanism. ConclusionsOur comparative analyses identified CRSP-encoding genes at the porcine CRSP complex locus as novel imprinted genes, indicating species-specific evolution of this imprinted domain. The results further suggest that lineage-specific gene duplication may have contributed to the emergence of imprinting at this locus.

genomics↗

bioRxiv2025

A standardized and reproducible behavioral protocol to elicit visual spatial attention in mice

Understanding how neural activity gives rise to cognitive processes such as selective attention is a fundamental goal of neuroscience. An important but often overlooked advance towards this goal requires the development and sharing of rigorous and reproducible behavioral tasks across labs; this is particularly important given the recent surge in studies of cognition and perception in mice. Here, we developed a standardized training protocol for head-fixed mice to become experts in a psychometric visual contrast detection task in just 17 days. Experts detected stimuli at two distinct spatial locations for several hundred trials per day. As consecutive trials elapsed at either location, the speed, accuracy, and contrast sensitivity of visual perception improved - all hallmarks of spatial attention improving performance, as seen in primates. These findings validate the efficacy of this protocol to reveal multiple aspects of selective spatial attention in mice, establishing a rigorous and reproducible tool for the community.

neuroscience↗

bioRxiv2025

Copper deficiency disrupts OXPHOS and mitochondrial dynamics through MTCH2-dependent copper trafficking in skeletal muscle

Copper is an essential trace element for mitochondrial respiration and cellular metabolism, yet its physiological role in skeletal muscle remains incompletely understood. Here, we show that skeletal muscle-specific deletion of the high-affinity copper importer Ctr1 (SMKO) in mice causes local copper deficiency, resulting in exercise intolerance, systemic metabolic dysfunction, and hallmarks of mitochondrial myopathy such as ragged-red fibers, lactic acidosis, and aberrant mitochondrial morphology. Mechanistically, copper starvation disrupted the electron transport chain proteome and drove pathological mitochondrial hyperfusion. We identified mitochondrial carrier homolog 2 (MTCH2), an outer mitochondrial membrane protein, as a copper-binding regulator that coordinates mitochondrial copper distribution and morphology. Restoring copper levels via a copper ionophore or AAV-mediated Ctr1 re-expression rescued mitochondrial function and alleviated myopathic features in SMKO. These findings uncover the functional coupling of CTR1 and MTCH2 as a critical mechanistic link between copper homeostasis and mitochondrial remodeling required for skeletal muscle function.

molecular biology↗

bioRxiv2025

De novo and scaffold-based design of GDF15 binders for cancer cachexia diagnostics and therapeutics

Growth differentiation factor 15 (GDF15), a stress-responsive cytokine of the TGF-{beta} superfamily, is elevated in cancer cachexia, chemotherapy-induced nausea, and hyperemesis gravidarum, making it both a biomarker and a therapeutic target. Here, we developed high-affinity GDF15 binders using an AI-driven protein design framework. To achieve this, we systematically explored three complementary scaffold-generation strategies: scaffold grafting (SG), diffusion-based de novo design, and scaffold-search and grafting (SSG), identifying distinct advantages - SG rapidly optimized receptor-derived motifs to subnanomolar affinity; de novo diffusion produced topologically novel binders; and SSG enabled access to GDF15s concave site B by repurposing evolutionary structural analogs from natural complexes. The designed GDF15 binders were translated into two functional modalities. First, a one-step, wash-free luminescent biosensor was created by coupling a de novo binder to split-luciferase fragments, enabling the rapid and sensitive quantification of GDF15. Second, the highest-affinity binder was engineered as an Fc-fusion decoy receptor, thereby effectively neutralizing GDF15 signaling in cell-based assays (IC50 = 7.2 nM), demonstrating comparable in vitro potency to ponsegromab, a monoclonal antibody currently undergoing Phase II clinical trials. Together, this work establishes a versatile AI-driven binder design pipeline with broad potential for next-generation diagnostics and therapeutics in cancer cachexia and other GDF15-mediated diseases.

bioengineering↗

bioRxiv2025

Aeon: an open-source platform to study the neural basis of ethological behaviours over naturalistic timescales

Ethological behaviours are a powerful tool for neuroscience since they leverage the robust neural computations shaped by the species evolution to study the neural basis of cognitive functions. However, such behaviours are often transitory and dependent on factors that vary over space, time and number of individuals, making them difficult to capture with standard laboratory tasks. Here we present Aeon, an open-source platform designed for continuous, long-term study of self-guided behaviours in multiple mice and simultaneous recording of brain activity within large, customizable habitats. By integrating specialized modules for navigation, nesting and sleeping, escaping, foraging, and social interaction, Aeon enables the expression of key ethological behaviours while achieving experimental control and multi-dimensional quantifications from sub-millisecond to month-long durations. Its software architecture ensures robust data acquisition via many synchronized data streams and delivers a new standardised, unified data format that yields seamless, integrated analysis pipelines. Using assays such as digging-to-threshold and social foraging, Aeon reveals how mice adapt strategies in a changing environment and in response to conspecifics. Aeon bridges ecological relevance with rigorous experimental control to advance our understanding of how neural circuit activity gives rise to a range of highly conserved and adaptive behaviours.

neuroscience↗

bioRxiv2025

Neural dynamics underlying the persistence of perseverative thought in depression and anxiety

Depression and anxiety are characterized by transdiagnostic symptoms, including perseverative thought: a class of thoughts such as rumination and worry that are negative, repetitive, and difficult to control. These thoughts contribute to substantial distress, poor treatment response, and increased risk of relapse. What makes perseverative thoughts persevere? Using task-based fMRI, we compared how adults with no lifetime psychopathology and adults with major depressive disorder, generalized anxiety disorder, or both, engaged top-down control processes to switch from personally-relevant perseverative or neutral thought to a working memory task. For only adults with clinical depression or anxiety, stopping perseverative thought was associated with more probable frontoparietal deactivation and more frequent default-mode activation versus stopping neutral thought. Using network control theory, we identified key control points that lead to these activity dynamics. We found that clinical perseverative thought elicited less controlled activity in the anterior cingulate cortex relative to thoughts in adults with no lifetime psychopathology, and lower control energy correlated with greater depression severity. The occipital-temporal, lateral prefrontal, and insular cortices also used less control energy in clinical perseverative thought. Low energy is characteristic of attractor states in dynamical systems theory, deep channels wherein the flow of activity naturally settles, analogous to how a ball needs little energy to roll to the bottom of a bowl yet more energy to leave it. Entrenchment in attractors provides a computational perspective on why top-down control signals relate to the persistence of clinical perseverative thought. These insights advance our understanding of the dynamic processes of perseverative thought, paving the way for novel interventions for depression and anxiety.

neuroscience↗

bioRxiv2025

Prg4+ fibro-adipogenic progenitors in muscle are crucial for bone fracture repair

Clinically, compromised fracture healing often occurs at sites with less muscle coverage and muscle flaps can provide the necessary healing environment for appropriate healing in severe bone loss. However, the underlying mechanisms are largely unknown. Here, we established a mouse reporter model for studying muscle cell contribution to bone fracture repair. Analyzing skeletal muscle scRNA-seq datasets revealed that Prg4 marks a fibro-adipogenic progenitor (FAP) subpopulation. In mice, Prg4+ cells were specifically located in the skeletal muscle, but not at the periosteum or inside cortical bone. These cells expressed FAP markers, responded to muscle injury, and became periosteal cells under normal and muscle injury conditions. Fracture fragmented muscle fibers, rapidly expanded Prg4+ FAPs at the injury site and promoted their migration into the fracture site. Later, they gave rise to many chondrocytes, osteoblasts, and osteocytes in the outer periphery of callus next to muscle. In repaired bones, the descendants of Prg4+ FAPs were detected as mesenchymal progenitors in the periosteum and osteocytes at the prior fracture site. A second fracture activated those cells and stimulated them to become osteoblasts in the inner part of callus. Importantly, ablation of Prg4+ FAPs impaired fracture healing and functional repair. In an intramembranous bone injury model (drill-hole), Prg4+ FAPs became periosteal cells, but their contribution to bone defect repair was significantly less than in fractures. Taken together, we demonstrate the critical role of FAPs in endochondral bone repair and uncover a novel mechanism by which mesenchymal progenitors transform from muscle to cortical bone. Significance statementFracture healing is often impaired in areas with less muscle coverage, but the mechanisms behind this are poorly understood. In this work, we uncovered a critical role of specific muscle cells, known as Prg4+ fibro-adipogenic progenitors (FAPs), in bone regeneration. Using mouse models, we show that these muscle-resident mesenchymal progenitors expand after bone injury, migrate to the fracture site, transform into various bone cells in the fracture callus, and eventually become bone surface progenitors after the bone is healed. This finding highlights the importance of muscle cells in endochondral fracture repair and reveals a novel crosstalk mechanism between muscle and bone tissues. Future studies targeting these muscle progenitor cells could develop new treatments for delayed and nonunion fractures.

cell biology↗

bioRxiv2025

Targeting the ITGA3B1 Complex with A Novel Antibody-Drug Conjugate for Metastatic Bladder Cancer

Advances in antibody (Ab) phage display technologies have enabled the development of targeted therapies with enhanced precision and clinical efficacy. Here, we report a phenotypic screening strategy combining target-unbiased live-cell biopanning with in situ chemical crosslinking and mass spectrometry to identify internalizing antibodies and their cognate antigens--key features for effective antibody-drug conjugate (ADC) development. Using this approach, we identified the 2E7 antibody, which exhibits rapid internalization and high specificity for the integrin 3{beta}1 (ITGA3B1) heterodimer, a complex overexpressed in multiple solid tumors, including bladder cancer. We generated an ITGA3B1-targeted ADC by conjugating monomethyl auristatin E (MMAE) to the 2E7 antibody, enabling selective delivery of cytotoxic payloads to ITGA3B1-positive cells. In preclinical bladder cancer models, this ADC demonstrated potent and dose-dependent antitumor efficacy, with significant tumor regression and improved survival. Our findings establish a framework for target discovery using live-cell phenotypic screening and position ITGA3B1 as a promising therapeutic target for ADC-based treatment of advanced bladder cancer. TeaserLive-cell biopanning uncovers ITGA3B1 as a target for ADC development in metastatic bladder cancer.

synthetic biology↗