Biology subjects

Kim, C.

Publications and source records attributed to Kim, C..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

A flow cytometry-based assay to quantify the binding of transmembrane ligands to their cognate receptors using fluorescent virus-like particles

The binding of transmembrane (TM) ligands to their cognate TM receptors on neighboring cells governs intercellular adhesion and direct cell-cell communication. However, these interactions are difficult to study in vitro because they depend on membrane presentation, ligand orientation, receptor clustering, and avidity, features often not captured by soluble recombinant ligands or cell-free assays. Here, we describe a flow cytometry-based assay using fluorescent, lentiviral-derived virus-like particles (VLPs) displaying TM ligands to quantify binding to their receptors on target cells. Fluorescent VLPs are generated in-house by plasmid transfection in HEK293T cells and enable direct fluorescent detection without fluorochrome-conjugated secondary antibodies. The system is modular and readily accommodates engineered ligand constructs, including patient-derived variants. We applied this platform to generate ICAM-1-displaying fluorescent VLPs and to study human LFA-1 function in patient-derived leukocytes. This protocol provides a detailed workflow for VLP production and in vitro binding assays, offering a simple, quantitative, and cost-effective approach for studying TM ligand-receptor interactions in a membrane context. The system is well suited for mechanistic studies, functional assessment of patient-derived variants, and direct binding assays using patient-derived cells. Integrating the assay into multicolor flow cytometry panels enables simultaneous immunophenotyping and quantification of up to four ligand-receptor interactions at single-cell resolution. Key featuresO_LIQuantifies TM ligand-receptor binding in a membrane context using fluorescent VLPs and flow cytometry. C_LIO_LIFully in-house, modular system based on plasmid transfection in HEK293T cells, without reliance on recombinant ligands or fluorochrome-conjugated secondary antibodies. C_LIO_LISupports testing of engineered ligand variants, including patient-derived alleles, and direct functional studies on patient-derived cells. C_LIO_LICompatible with multicolor flow cytometry panels, enabling simultaneous immunophenotyping and quantification of up to four ligand-receptor interactions at single-cell resolution. C_LI Graphical overview O_FIG O_LINKSMALLFIG WIDTH=197 HEIGHT=200 SRC="FIGDIR/small/725198v1_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@a43069org.highwire.dtl.DTLVardef@166491borg.highwire.dtl.DTLVardef@49c7d4org.highwire.dtl.DTLVardef@1de36a0_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2026

Systematic profiling of WD40 proteins reveals Wcp1, a cyclophilin linking CO2/heat tolerance to acidic pH adaptation in Cryptococcus neoformans

WD40 domains are major protein-protein interaction (PPI) scaffolds, yet their contributions to fungal pathogenicity remain poorly defined. We systematically analysed 94 canonical WD40 proteins in Cryptococcus neoformans. Conditional knockdown and sporulation identified 36 essential WD40 proteins, while in vitro and in vivo profiling of 103 signature-tagged deletion strains spanning 52 genes uncovered 31 pathogenicity-related WD40 proteins, including epigenetic and post-transcriptional regulators. We identified Wcp1, a dual-domain protein whose WD40-repeat and cyclophilin domains are required for growth at 37{degrees}C under 5% CO2. Its WD40 scaffold and PPIase domain supported CO2/heat tolerance and virulence. Notably, Wcp1 couples these functions to acidic pH adaptation: wcp1{Delta} failed to grow under elevated temperature and CO2 at acidic pH, exhibited enhanced intracellular acidification, reduced macrophage survival and attenuated virulence in Drosophila and mice. Integrated transcriptomic and proteomic analyses place Wcp1 at the centre of intracellular pH homeostasis, coordinating proton transport, metabolic adaptation and stress-buffering networks.

microbiology↗

bioRxiv2026

Aerosol delivery-based serial femtosecond crystallography

Serial femtosecond crystallography (SFX) has revolutionised structural biology by enabling direct visualization of conformational dynamics of biomacromolecules at near-physiological temperatures. However, conventional SFX sample delivery at X-ray free-electron laser (XFEL) facilities introduces a significant X-ray scattering background, which may limit the data quality and resolution. Here, we introduce an aerosol delivery-based method that drastically reduces the back-ground scattering by minimising the liquid environment surrounding the nanocrystals. We validate our method by solving the structure of Cydia pomonella granulovirus nanocrystals at 1.9 [A] resolution, achieving orders-of-magnitude lower background scattering compared to a liquid jet-based method. Structural comparison with the liquid jet-based model revealed similar overall structure, suggesting that the native structure is largely preserved despite dehydration during aerosolisation. Our method enables efficient SFX studies, particularly pump-probe time-resolved SFX on protein nanocrystals with enhanced signal-to-noise ratios, as well as high-throughput small molecule SFX (smSFX) applications for pharmaceuticals and functional materials.

biophysics↗

bioRxiv2026

3-Minute Hematoxylin and Oil Red O (H-ORO) Staining Protocol for Frozen Sections of Zebrafish

Optimized histological techniques are crucial for visualizing cellular morphology across zebrafish tissues. Here, we report a rapid and reliable hematoxylin and Oil Red O (H-ORO) staining protocol for frozen sections that can be completed in less than three minutes. Mayers hematoxylin is used for nuclear staining, followed by Oil Red O (ORO) to visualize lipid-rich structures such as the endomysium surrounding myofibers, white matter of the brain, and myelin layers of major axonal tracts. Importantly, our optimized H-ORO protocol preserves tissue integrity and minimizes artifacts such as myofiber shrinkage commonly observed with ethanol-based hematoxylin and eosin (H&E) staining in both frozen and paraffin sections.

pathology↗

bioRxiv2026

PA-SfM: Tracker-free differentiable acoustic radiation for freehand 3D photoacoustic imaging

Three-dimensional photoacoustic imaging (3D PAI) has shown great potential in preclinical studies and clinical implementations, while it commonly has sparse sensor arrays, limiting both spatial sampling and the field of view (FOV). Freehand scanning could overcome these limitations through anatomy-adaptive scanning that extends spatial coverage and provides complementary views beyond the fixed array aperture, but its flexibility is conventionally constrained by the need for motor feedback or external pose tracking. Here we introduce PA-SfM, a tracker-free structure-from-motion (SfM) framework that recovers multiple poses directly from PA measurements with superior precision, enabling freehand 3D PAI without external pose measurements. PA-SfM integrates a differentiable acoustic radiation model with hierarchical optimization and rigid array constraints, it jointly estimates inter-view transformations and reconstructs 3D volumes. The performance of PA-SfM was demonstrated in numerical simulations, animal studies and human imaging experiments. Compared with motor encoder-based fusion of the mechanically scanned system, PA-SfM produced sharper and more continuous vascular reconstructions with an expanded FOV. In controlled quantitative validations, PA-SfM achieved high reconstruction fidelity, with PSNR values over 40 dB and SSIM values above 0.98 relative to ground truth or known pose reference reconstructions. These results demonstrate that PA-SfM enables robust freehand 3D PAI, with particular potential for clinical implementation of large-scale freehand imaging. The source code is publicly available at https://github.com/JaegerCQ/PA-SfM.

bioengineering↗

bioRxiv2026

Control of cell division by an Acinetobacter baumannii protein with a novel nucleotidyl-cyclase-like fold

The antibiotic-resistant pathogen Acinetobacter baumannii has diverged from model {psi}-proteobacteria in fundamental ways, complicating the development of new antimicrobial strategies. A major area of divergence is cell division. A. baumannii lacks several widely conserved division enzymes, such as FtsEX, and instead possesses a suite of atypical gene products with no similarity to well-characterized proteins. Key among these is AdvA, which we previously identified by Tn-seq as essential for A. baumannii division and fluoroquinolone resistance. The protein comprises an N-terminal transmembrane/periplasmic region connected to a C-terminal unannotated cytoplasmic domain, and most advA transposon insertions were lethal unless they occurred within the linker between these regions. The roles of AdvA in cell division and the basis for these positional transposon effects were unclear. Here, we combine mutagenesis with fluorescence localization, two-hybrid, and structural analyses to define how AdvA domains function in assembling and activating the A. baumannii divisome. AdvA depletion profoundly disrupts divisome construction at Z-rings. This dependence reflects numerous interactions with divisome proteins, with AdvAs N-terminal region binding multiple components and cytoplasmic domain binding one, the early protein ZipA. In addition, we identified substitutions in FtsB and FtsW that suppress AdvA essentiality, consistent with a role in divisome activation as well as recruitment. Finally, we determined the structure of the cytoplasmic domain, revealing a novel adenylyl/guanylyl cyclase-like fold that lacks canonical catalytic and dimerization sites and instead features a positively charged tip key to fluoroquinolone resistance and a C-terminal helix essential to division. The critical C-terminal structure helps explain the positional transposon effects and facilitated identification of a distant homolog in Pseudomonas aeruginosa. These results reveal a new control protein governing bacterial division that could be exploited to combat nosocomial infections. ImportanceThe multidrug-resistant sepsis pathogen Acinetobacter baumannii poses an urgent threat to public health. Fundamental features of its cell cycle, such as how it controls cell division, are not well understood, but this information could lead to improved antimicrobial strategies. We demonstrate that a protein (AdvA) bearing a previously unrecognized structure has a critical role in cell division and fluoroquinolone antibiotic resistance in the pathogen. The structure resembles the nucleotide cyclase class of enzymes, but it has lost the typical catalytic properties and instead uses novel sites to enable assembly and activation of the cell division machine. The novel fold is found in other pathogens such as Pseudomonas aeruginosa, in which it is also connected to drug resistance and cell division. This work opens new avenues to understand and interrupt cell division in multidrug-resistant hospital-acquired bacteria.

microbiology↗

bioRxiv2026

Title: Optogenetic WNT signaling drives germ layer self-organization in a human gastruloid model

In vitro stem cell models of human gastrulation have been an advance for developmental biology, though elucidating mechanisms of germ layer formation remains challenging. While investigating whether spatially-patterned signaling is required for germ layer formation, we tested a "salt-and-pepper" signaling strategy in which WNT was optogenetically activated in a subset of human pluripotent stem cells (hPSC) uniformly mixed into an aggregate. Following mesendodermal specification, WNT-activated cells spatially segregated into a hemisphere, then underwent further differentiation and organization into mesoderm and endoderm. RNAseq-based lineage analysis revealed that WNT activation non-autonomously induced TGF{beta}/BMP signaling, leading to robust emergence of an anterior visceral endoderm-like population that patterned adjacent neural and mesendodermal fates. Transcriptional profiles and trajectories closely mirrored those observed during human gastrulation. Moreover, TGF{beta} or cadherin perturbation disrupted germ layer formation or spatial organization, respectively. This simple model thus enables mechanistic dissection of complex human lineage specifications and organization during gastrulation.

bioengineering↗

bioRxiv2026

De novo design of a safe and potent respiratory syncytial virus immuno-focusing antigen

Respiratory syncytial virus (RSV) remains the leading cause of severe respiratory infections in infants, the elderly, and the immunocompromised. Although stabilized full-length pre-fusion (pre-F) protein vaccines are promising, enhanced respiratory disease (ERD) remains a critical safety concern. Here, we used artificial intelligence to design a de novo immuno-focused antigen that structurally preserves the RSV F head region containing critical neutralising epitopes-- site O, II and V-while replacing the non-neutralising stem with a computationally designed scaffold to minimise immunopathological risk. The lead candidate, aRF6, elicited robust protective immunity against RSV in mice and similar immunogenicity in non-human primates without detectable toxicity. Importantly, in stringent ERD-promoting models, aRF6 induced minimal pulmonary pathology and markedly attenuated Th2-biased cytokine responses, outperforming formalin-inactivated RSV and full-length-stabilized pre-F. The results of cryoelectron microscopy confirmed that the aRF6 structure precisely matched the computational predictions. These results demonstrated that computationally designed de novo immuno-focused antigens can yield safe and effective RSV vaccines, thereby providing a rational framework for next-generation vaccine development.

microbiology↗

bioRxiv2026

FLInt 2.0: Robust and customizable single shot integration in C. elegans

Transgenesis in Caenorhabditis elegans has revolutionized biological research by enabling the precise control of expression of both endogenous and exogenous genes. The FLInt (Fluorescent Landmark Interference) method was developed to accelerate site-specific integration of transgenes, but persistent false-positive events during screening have emerged as a rate-limiting step. Here, we present an alternative FLInt strategy, FLInt 2.0, that reduces false positives by biasing Cas9 cutting of the tdTomato and Cbr unc-119(+) safe-harbor locus, adjacent to the untranslated region (3 UTR). The design preserves fluorescence during non-integrative repair events, such that only true integration of an extrachromosomal array abolishes tdTomato expression. We demonstrate that this targeted approach maintains high integration efficiency while significantly decreasing the proportion false positives observed in F1 progeny. Molecular and transmission analyses confirm that non-fluorescent F2 animals reliably represent stably integrated multi-copy transgenic lines, which can be tailored to desired expression levels using a simple subsequent Cas9 targeting approach. By exploiting coding-frame geometry to discriminate integration events from repair-induced artifacts, this method streamlines the identification of the true integrants, reducing labor-intensive screening and increasing experimental throughput. Our strategy provides a robust, visually guided, and efficient refinement of FLInt, offering a generalizable framework for improving site-specific transgene integration in C. elegans.

genetics↗

bioRxiv2026

Inflammatory signaling differentially changes chromatin accessibility and gene expression of the PD- associated kinase LRRK2 between human and mice

The genomic locus that encodes the Leucine-rich repeat kinase 2 (LRRK2) gene is highly pleiotropic, being associated with both Parkinsons disease (PD) and Crohns disease (CD). Coding variants associated with risk of PD and CD act as gain of function kinase mutations increasing phosphorylation of RAB substrates, and non-coding variants in the promoter region of LRRK2 increase expression of the gene, notably in immune cells. If regulation of LRRK2 expression is a causal contributor to age-related diseases, it is important to understand the mechanism(s) by which LRRK2 is regulated, particularly in the context of inflammation. Here, we show that interferon-{gamma} exposure induces robust LRRK2 activation in human iPSC-derived microglia through signaling of the Janus-activated Kinase complex to phosphorylate STAT1, which then binds to the LRRK2 promoter and is associated with remodeling of chromatin structure in this genomic locus. Additional regulatory mechanisms include the stress-induced transcription factor and long non-coding RNA encoded at the same locus, resulting in increased LRRK2 mRNA levels. We also show evidence of the same effect in acutely cultured human brain slices. While we were unable to demonstrate any induction of Lrrk2 mRNA in the mouse brain, the introduction of a human bacterial artificial chromosome transgene into the mouse genome recapitulated sensitivity to interferon-{gamma} in microglia. A comparative genomic analysis across mammals suggests that these species differences are driven by regulatory regions upstream of LRRK2 that are specific to anthropoid primates. These results demonstrate that there are differences between species in how genes associated with human diseases are regulated and provide important information that should be incorporated in disease modeling.

neuroscience↗

bioRxiv2026

YAP activation reverses aging-related visual dysfunction caused by impaired cell-matrix adhesion

Cellular senescence of retinal pigment epithelium (RPE) cells drives age-related visual decline, particularly in the pathology of age-related macular degeneration (AMD). While genome-wide association studies (GWAS) have identified genetic risk factors underlying AMD, the molecular mechanisms governing RPE senescence remain unclear. Here, single-cell RNA sequencing of young and old mouse RPE revealed dysregulated cell-matrix adhesion as a key feature of senescence, consistent with transcriptional changes in AMD patients. Hydrogel-based experiments confirmed that impaired integrin-mediated adhesion induces RPE senescence. Yes-associated protein 1 (YAP), a crucial mechanotransducer, mediated the protective effects of cell-matrix adhesion, and its activation alone reversed aging phenotypes in senescent RPE cells. Notably, treatment with TRULI, a small-molecule YAP activator, significantly improved visual function in AMD and naturally aged mice. These findings highlight the integrin-YAP mechanotransduction pathway as a fundamental regulator of RPE senescence and a potential therapeutic target for AMD.

physiology↗

bioRxiv2025

Functional Characterization of 123 Genes from Mycobacteriophage LeBron Uncovers Cytotoxic Gene Families in Cluster L1

Bacteriophages represent a vast reservoir of genetic diversity however, functional annotation remains a major challenge, as most predicted gene products lack detectable similarity to characterized gene families. Experimental approaches such as systematic overexpression screens provide an avenue for identifying phage genes that influence bacterial physiology. Here, we report an overexpression screen of all 123 predicted protein-coding genes from Cluster L1 mycobacteriophage LeBron, the first representative of this cluster to undergo genome-wide functional analysis. Expression assays in Mycobacterium smegmatis revealed that 39 genes (32%) impaired host growth, with nineteen of these toxic genes (49%) assigned no known function. The proportion of cytotoxic genes observed in LeBron is comparable to findings from Clusters K and F, despite minimal sequence conservation across clusters. Interestingly, a subset of LeBrons toxic genes appear to be functionally analogous to previously identified toxic genes in other clusters, suggesting conserved biological activities carried out by non-homologous proteins. Additionally, this analysis uncovered several novel gene families that elicit strong cytotoxic effects, expanding the known catalog of phage-derived bacterial growth inhibitors. These results provide new insights into phage gene functions and demonstrate the value of genome-wide expression screening for uncovering conserved and cluster-specific interactions between bacteriophages and their hosts.

microbiology↗

bioRxiv2025

Comparing the evolvability of an ancestrally reconstructed and modern adenylate kinase

Directed evolution transformed protein engineering by providing a customizable framework for generating enzymes with improved catalytic performance across diverse functions. Yet modern enzymes often stall during directed evolution because populations become trapped on local fitness peaks. Researchers have suggested that ancestral enzymes offer better starting points because they are typically more thermostable. Here we propose and experimentally test an alternative explanation that does not depend on ancestral thermostability. We posit that ancestrally reconstructed sequences are unusually evolvable because they are inferred from the evolutionary lineages that survived to produce extant proteins. Less evolvable ancestors, and the trajectories emanating from them, disappeared by extinction and therefore do not contribute to reconstructed ancestors. Using thermophilic ancestral and modern adenylate kinases, we performed independent single-round selection experiments for activity in vivo and in vitro. In both settings, the ancestral enzyme tolerates a larger number of mutations, yielding more viable variants with greater genetic diversity than its modern descendants. Because mutational robustness promotes evolvability, these results support an intrinsic evolvability of reconstructed ancestral sequences that makes them superior launch points for directed evolution.

biochemistry↗

bioRxiv2025

Mammary Fibroblasts Secrete Damage Associated Molecular Patterns through Extracellular Vesicles in Response to Ionizing Radiation

Ionizing radiation (IR) is an integral component of cancer therapy. Cellular exposure to IR typically leads to major biological consequences including cell death and senescence. Furthermore, tissue injury in known to involve the release of damage-associated molecular patterns (DAMPs) into the extracellular space, which trigger inflammation and wound healing. However, DAMP release in the context of radiation injury remains to be fully characterized. Evidence suggests that extracellular vesicle (EV) secretion and associated cargo components are part of the cellular response to IR, but the mechanisms integrating cellular damage and EV secretion post-IR are largely unexplored. In this study, we show that acute IR-induced damage in mammary fibroblasts results in a senescence-like phenotype and substantially increased EV secretion. Quantitative proteomic analysis revealed that IR-induced EVs are enriched with extracellular and intracellular DAMPs, along with other pro-inflammatory mediators. We show that knockdown of the GTPase Rab27a abrogates IR-induced EV secretion and inhibits the enrichment of key DAMPs in EVs. By examining the integration of cellular damage and senescence with the release of inflammatory signals, this study elucidates a potentially critical role for EV-associated proteins in the radiation response.

cancer biology↗

bioRxiv2025

3D Hybrid Bioprinting for Complex Multi-Tissue Engineering

3D bioprinting has revolutionized tissue engineering, enabling intricate, physiologically relevant constructs unattainable with conventional techniques, yet it remains limited in integrating soft and rigid multifunctional components for complex multi-tissue applications. In this study, we introduce a 3D hybrid bioprinting approach implementing the Hybprinter platform, which integrates multiple 3D printing modules under optimized conditions for a continuous bioprinting process with multiple soft and hard biomaterials. This approach demonstrates robust biocompatibility and broad tissue engineering potential for modeling and therapeutic applications. The capacity to fabricate multi-hydrogel hybrid constructs is illustrated by representative examples highlighting vascularization, multifunctionality, mechanical robustness, and implant suturability. Notably, compared with commonly fabricated hydrogel-only constructs, the resulting hybrid constructs achieve over a 1000-fold increase in mechanical strength, and demonstrated enhanced osteogenic differentiation, underscoring their suitability for load-bearing musculoskeletal and orthopedic tissue engineering. Additionally, cell-laden hydrogel constructs demonstrated robust chondrogenic differentiation, highlighting the capacity for lineage-specific tissue development in vitro. Beyond these outcomes, the presented hybrid bioprinting approach integrates essential tissue engineering attributes that unites mechanical robustness and suturable capacity with multi-material integration, gradient property design, incorporation of bioactive agents, and support for multi-cell loading. This versatile platform advances complex tissue engineering and holds promise for patient specific, organ-on-demand applications.

bioengineering↗

bioRxiv2025

Role of tankyrase scaffolding in the β-catenin destruction complex and WNT signaling

Aberrant WNT/{beta}-catenin signaling drives tumorigenesis and metastasis in cancer. Although enzymatic inhibitors of tankyrase (TNKS) effectively block AXIN degradation and stabilize the {beta}-catenin destruction complex (DC), they have demonstrated limited efficacy in various cancer models. Here we demonstrate that, unexpectedly, the induction of AXIN puncta represents a major barrier to achieving therapeutic efficacy. Mechanistically, catalytic inhibition of TNKS prevents TNKS turnover and drives its accumulation in the DC, wherein the scaffolding function of TNKS induces AXIN puncta formation, rigidifies the DC, and impedes {beta}-catenin turnover. Chemically induced degradation of TNKS overcomes this limitation by stabilizing AXIN without puncta formation, providing a deeper suppression of the WNT/{beta}-catenin pathway activity and the proliferation of colorectal cancer cells harboring dysfunctional APC mutations. Collectively, these findings provide an explanation for the unsatisfactory outcomes of drugging the WNT/{beta}-catenin signaling pathway by TNKS inhibitors and highlight TNKS degradation as a promising approach to treat WNT/{beta}-catenin-driven cancers.

cancer biology↗

bioRxiv2025

Nanoscopy of Organelle Handoff Portals Reveals Direct Coupling between ER Remodeling and Microtubule-Based Transport

How biosynthetic organelles leave the endoplasmic reticulum (ER) and engage with microtubule tracks remains a central question. Combining interferometric scattering with fluorescence nanoscopy, we tracked nanometer-scale handoff events in living cells. ER-derived organelles undergo biased diffusion along ER tubules toward nearby microtubules. ER three-way junctions function as nanoscopic hubs where cargo pauses, contacts multiple microtubules, and then launches onto a track for long-range travel. Remarkably, the ER maintains a membrane tether to the departing cargo, extending its tubules and forming new junctions, thereby coupling inter-network transfer with membrane morphogenesis. These observations reveal an integrated mechanism that links organelle biogenesis, directional trafficking, and continual ER- and cellular remodeling, underscoring the ERs active role in steering transport and repurposing its own output within the crowded intracellular environment.

cell biology↗

bioRxiv2025

Paracrine Bone-Derived Senescent Secretome Induces Spatially Patterned ECM and Biomechanical Vulnerability in Human Brain Organoids

Aging is increasingly recognized as a systemic process, yet the mechanisms by which senescent cells signal from peripheral tissues accelerate brain aging remain poorly defined. Here, we used chronic exposure of human cerebral organoids to the secretome of senescent osteocytes to investigate how peripheral aging signals reshape brain tissue architecture. We combined spatially resolved optical fiber-based interferometry nanoindentation with transcriptomic and immunofluorescence profiling, demonstrating that bone-derived senescence-associated secretory phenotype (SASP) factors induce a biphasic mechanical response, early global tissue softening, followed by the emergence of discrete hyper-stiff microdomains. This spatially heterogeneous biomechanical remodeling was accompanied by upregulation of extracellular matrix (ECM), inflammatory, and senescence pathways, and suppression of neurodevelopmental and synaptic gene networks. Our results reveal that chronic paracrine SASP exposure from senescent osteocytes drives localized ECM reorganization and mechanical vulnerability in human brain tissue, providing mechanistic insight into how peripheral cellular senescence may contribute to regional brain fragility during aging.

bioengineering↗