Biology subjects

Kim, B. G.

Publications and source records attributed to Kim, B. G..

7 recordsLinked to original sources

bioRxiv2026

Water oxidation-driven histidine dioxidation enables probe-free proximity labeling

Photocatalytic proximity labeling (photo-PL) has emerged as a powerful tool for spatial proteomics in subcellular compartments. However, many photo-PL toolboxes rely on singlet oxygen (1O2) to generate highly unstable endoperoxide intermediates that must be trapped immediately by high concentrations of exogenous probes. This constraint can bias spatial proteome coverage, particularly in dynamic and heterogeneous compartments such as endosomes and exosomes, where probe accessibility is intrinsically nonuniform. Here, we develop IDM, an organic photocatalyst that generates hydroxyl (*OH) and superoxide (O *-) radicals via water oxidation instead of 1O , enabling a synergistic dual-radical mechanism for probe-free proximal protein mapping in live cells (PF-Map). The resulting radicals dioxidize proximal histidine residues into a persistent dioxidized state (His-2O) that is thermodynamically stabilized as lactam tautomers, which remain electrophilic and chemically addressable after cell lysis. By decoupling histidine oxidation from live{square}cell probe capture, PF{square}Map can minimize spatial bias arising from heterogeneous probe distribution. Applying PF{square}Map to intracellular vesicle trafficking, we find that both PF{square}Map and a probe{square}dependent workflow (PD{square}Map) robustly identify exosome markers, whereas PF{square}Map additionally reveals a hidden vesicle trafficking-related subproteome that PD-Map underestimated. Together, we establish a minimally biased photocatalytic strategy for spatial protein mapping in complex biological systems. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/731337v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@13da43dorg.highwire.dtl.DTLVardef@1e9cb7corg.highwire.dtl.DTLVardef@2e7557org.highwire.dtl.DTLVardef@19e16c_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Novel mouse model of cerebral microbleeds created by Crispr/Cas9-mediated Col4a1 deletion in adult brain microvessels

Cerebral small vessel disease is a leading cause of cognitive decline and stroke in the elderly, with cerebral microbleeds (CMBs) as one of the key imaging biomarkers. Our understanding of its pathophysiology remains limited due to the lack of appropriate animal models. We report a novel mouse CMB model created by disrupting collagen IV, a core component of the vascular basement membrane (BM), specifically within brain microvessels. Targeted deletion of Col4a1 was achieved in adult mice using brain endothelial-specific AAV vectors with CRISPR/Cas9. MRI revealed numerous CMBs with distributions similar to those of human CMBs. CMB burden increased progressively over six months following Col4a1 deletion in a dose-dependent manner, accompanied by cognitive decline and motor incoordination. Histological examination revealed hemosiderin deposits corresponding to MRI-detected CMBs without evidence of macroscopic hemorrhage or white matter lesions, while ultrastructural analysis demonstrated significant BM thinning in Col4a1-depleted microvessels. Analysis of human MRI and genomic data identified significant associations between CMB susceptibility and genetic variants in TIMP2, an endogenous inhibitor of the matrix-degrading enzyme MMP2, underscoring the clinical relevance of our model. These findings establish a direct causal relationship between microvessel COL4A1 and CMB, suggesting that dysregulated collagen IV homeostasis in BM underlies CMB development.

neuroscience↗

bioRxiv2025

Mechanical environment afforded by engineered polymer hydrogel critically regulates survival of neural stem cells transplanted in the injured spinal cord via Piezo1-mediated mechanotransduction

Neural stem cell (NSC) transplantation is a promising therapeutic approach for spinal cord repair, but poor graft survival remains a critical challenge. Here, we demonstrate that the mechanical properties of the transplantation microenvironment play a crucial role in NSC survival in the injured spinal cord. While our previously engineered imidazole-poly(organophosphazene) (I-5) hydrogel effectively prevented cavity formation by promoting extracellular matrix remodeling, NSCs transplanted with 10% hydrogel exhibited poor survival. Remarkably, increasing the hydrogel concentration to 16%, which created a 5-fold stiffer matrix, significantly enhanced NSC graft survival and synaptic integration. Using in vitro models with controlled substrate stiffness, we found that NSCs on stiffer substrates displayed enhanced adhesion, complex morphology, and increased viability. Importantly, we identified the mechanosensitive ion channel Piezo1 as the key molecular mediator of these stiffness-dependent behaviors. CRISPR/Cas9-mediated Piezo1 gene editing in NSCs significantly reduced graft survival in vivo when transplanted with 16% hydrogel, confirming that Piezo1-mediated mechanotransduction is essential for NSC survival in the injured spinal cord. Our findings reveal a previously unrecognized mechanism governing graft survival in the injured spinal cord and suggest that optimizing the mechanical properties of biomaterial scaffolds or targeting Piezo1-dependent mechanotransduction could substantially improve outcomes of cell-based therapies for neurological disorders.

neuroscience↗

bioRxiv2024

Detrimental Influence of Arginase-1 in Infiltrating Macrophages on Post-Stroke Functional Recovery and Inflammatory Milieu

Post-stroke inflammation critically influences functional outcomes following ischemic stroke. Arginase-1 (Arg1) is conventionally understood as a marker for anti-inflammatory macrophages, associated with the resolution of inflammation and promotion of tissue repair in various pathological conditions. However, its specific role in post-stroke recovery remains to be elucidated. This study investigates the functional impact of Arg1 expressed in macrophages on post-stroke recovery and inflammatory milieu. We observed a time-dependent increase in Arg1 expression, peaking at 7 days after photothrombotic stroke in mice. Cellular mapping analysis revealed that Arg1 was predominantly expressed in LysM-positive infiltrating macrophages. Using a conditional knockout (cKO) mouse model, we examined the role of Arg1 expressed in infiltrating macrophages. Contrary to its presumed beneficial effects, Arg1 cKO in LysM-positive macrophages significantly improved skilled forelimb motor function recovery after stroke. Mechanistically, Arg1 cKO attenuated fibrotic scar formation, enhanced peri-infarct remyelination, and increased synaptic density while reducing microglial synaptic elimination in the peri-infarct cortex. Gene expression analysis of FACS-sorted microglia revealed decreased TGF-{beta} signaling and pro-inflammatory cytokine activity in peri-infarct microglia from Arg1 cKO animals. In vitro co-culture experiments demonstrated that Arg1 activity in macrophages modulates microglial synaptic phagocytosis, providing evidence for macrophage-microglia interaction. These findings provide new insights into Arg1 function in CNS injury and highlight an interaction between infiltrating macrophages and resident microglia in shaping the post-stroke inflammatory milieu. Our study identifies Arg1 in macrophages as a potential therapeutic target for modulating post-stroke inflammation and improving functional recovery.

neuroscience↗

bioRxiv2023

A primary culture method for the easy, efficient and effective acquisition of oligodendrocyte lineage cells

Oligodendrocytes (OL) are myelin forming glial cells in the central nervous system. In vitro primary OL culture models provide the benefit of a more readily controlled environment facilitating the evaluation of diverse OL stages and convoluted dynamics. Conventional methods of primary OL culture do exist, but their performance in terms of efficiency and simplicity has room for improvement. We present a novel method of primary OL culture, namely the E3 (Easy, efficient, and effective) method, which greatly improves cell yield and reduces time required to oligodendrocyte progenitor cell (OPC) acquisition and maturation into OLs. We also provide optimal media compositions for augmentation of OPC proliferation and a more robust maturation into myelin forming OLs. In vitro characteristics of the OL lineage discovered during the development of the E3 method present implications for further research on OL physiology and pathophysiology.

neuroscience↗

bioRxiv2021

Oncomodulin derived from regeneration-associated macrophages in dorsal root ganglia promotes axon regeneration in the spinal cord

Preconditioning nerve injury drives pro-regenerative perineuronal macrophage activation in dorsal root ganglia (DRG). The present study reports that oncomodulin (ONCM) is produced from the regeneration-associated macrophages (RAMs) and strongly influences regeneration of DRG sensory axons. Preconditioning injury upregulated ONCM in DRG macrophages in a CCR2 dependent manner. ONCM in macrophages was necessary to produce RAMs in the in vitro model of neuron-macrophage interaction and played an essential role in for preconditioning or CCL2-induced neurite outgrowth. ONCM potently increased neurite outgrowth in cultured DRG neurons by activating a distinct gene set, particularly neuropeptide-related genes. Increasing extracellularly secreted ONCM in DRGs sufficiently enhanced capacity of neurite outgrowth. To achieve sustained ONCM activity in vivo, recombinant ONCM was encapsulated by a reducible epsilon-poly(L-lysine)-nanogel (REPL-NG) system based on electrostatic interaction. Localized injection of REPL-NG/ONCM complex into DRGs achieved a remarkable long-range axonal regeneration beyond spinal cord lesion, surpassing the extent of the preconditioning effects.

neuroscience↗

bioRxiv2021

Analysis of B-cell receptor repertoires in COVID-19 patients using deep embedded representations of protein sequences

Analyzing B cell receptor (BCR) repertoires is immensely useful in evaluating ones immunological status. Conventionally, repertoire analysis methods have focused on comprehensive assessments of clonal compositions, including V(D)J segment usage, nucleotide insertions/deletions, and amino acid distributions. Here, we introduce a novel computational approach that applies deep-learning-based protein embedding techniques to analyze BCR repertoires. By selecting the most frequently occurring BCR sequences in a given repertoire and computing the sum of the vector representations of these sequences, we represent an entire repertoire as a 100-dimensional vector and eventually as a single data point in vector space. We demonstrate that this new approach enables us to not only accurately cluster BCR repertoires of coronavirus disease 2019 (COVID-19) patients and healthy subjects but also efficiently track minute changes in immune status over time as patients undergo treatment. Furthermore, using the distributed representations, we successfully trained an XGBoost classification model that achieved a mean accuracy rate of over 87% given a repertoire of CDR3 sequences.

bioinformatics↗