Biology subjects

Koo, H.

Publications and source records attributed to Koo, H..

9 recordsLinked to original sources

bioRxiv2026

Emulating the gingival-tooth interface during bacterial, fungal, and viral infection in a microphysiological model of the human oral cavity

The anatomical complexity and distinctive tissue environment of the human oral cavity pose major challenges to modeling oral infection and host-microbe interactions in preclinical laboratory settings. Here we present a bioengineered oral microphysiological system comprising vascularized human gingival tissue integrated with tooth analogs that together recreate a functional unit of the human oral cavity. We incorporated Streptococcus mutans and Candida albicans into this system to model cross-kingdom biofilm formation, microbial dissemination, and host-microbial interactions at the gingival-tooth interface. Single-cell RNA sequencing and global metabolomics analysis revealed that fungal colonization induces epithelial-to-mesenchymal transition associated with distinct transcriptional and metabolic signatures. Our platform also allowed us to simulate SARS-CoV-2 infection and examine gingival responses to live-virus challenge. Finally, we integrated the engineered gingival tissue with controlled human saliva flow to show that hyposalivation potentiates the pathogenic capacity of fungal infection. This work demonstrates the potential of oral microphysiological systems as an experimental platform for in vitro modeling and mechanistic investigation of host-microbe interactions under controlled, human-relevant conditions.

bioengineering↗

bioRxiv2025

GPR37 activation erases spinal pain memory and resolves increased nociception in murine models

Intense injury induces long-term changes in the spinal nociceptive system, which increases pain in magnitude and duration. We investigated whether activation of G protein-coupled receptor 37 (GPR37) at the spinal level can erase this nociceptive system sensitization and resolve long-lasting, enhanced pain using two animal models: the capsaicin model and the hyperalgesic priming model. Without altering normal mechanical and heat nociception, a single intrathecal (i.th.) administration of two GPR37 agonists, TX14A and protectin D1 (PD1), dose-dependently inhibited capsaicin-induced increase in nociception not only acutely but also long-term. In the hyperalgesic priming model, a single i.th. injection of either GPR37 agonist after an initial injury-induced priming dose-dependently prevented increased nociception following a subsequent inflammatory insult, indicating an unpriming effect. Global GPR37 knockout or conditional knockout of GPR37 in TRPV1-lineage sensory neurons abolished the long-term inhibitory effect and unpriming effect of i.th. TX14A, confirming that GPR37 in this specific cellular population mediates these effects. Ex vivo Ca{superscript 2} imaging revealed that i.th. TX14A, given in vivo to the capsaicin model a week before imaging, had rescued dorsal horn excitatory and inhibitory interneurons from long-term potentiation and depression of responsiveness to afferent inputs, respectively, suggesting the erasure of capsaicin-induced nociceptive system sensitization. Conditioned place preference tests indicated no obvious abuse liability for centrally administered GPR37 agonists. These findings suggest that spinally targeting GPR37 in TRPV1-expressing sensory neurons represents a promising therapeutic strategy for resolving persistent pain by erasing nociceptive system sensitization.

neuroscience↗

bioRxiv2025

Scalable flow synthesis of ultrasmall inorganic nanoparticles for biomedical applications via a confined impinging jet mixer

Ultrasmall inorganic nanoparticles (sub-5 nm) have unique biomedical advantages due to rapid clearance, enhanced imaging contrast, and potent therapeutic properties. However, current synthesis methods are limited by low throughput, polydispersity, and reliance on harsh conditions such as organic solvents or high temperatures. We report a scalable, single-step aqueous synthesis using a confined impinging jet mixer (CIJM) that produces size-controlled, clinically relevant nanoparticles, including silver sulfide, silver telluride, cerium oxide, and iron oxide, under ambient conditions. The resulting nanoparticles are homogeneous, stable, and preserve their functional biological properties. We demonstrate consistent performance across scales, establishing the CIJM as a versatile and reproducible method for producing ultrasmall inorganic nanoparticles suitable for clinical translation and high-throughput biomedical applications.

bioengineering↗

bioRxiv2024

PAM-flexible adenine base editing rescues hearing loss in a humanized MPZL2 mouse model harboring an East Asian founder mutation

Hearing loss is one of the most prevalent sensory disorders, but no commercial biological treatments are currently available. Here, we identified an East Asia-specific founder mutation, the homozygous c.220C>T mutation in MPZL2, that contributes to a significant proportion of hereditary deafness cases in our cohort study. We found that the disease-causing mutation could be targetable by adenine base editors (ABEs) that enable A{middle dot}T-to-G{middle dot}C base corrections without DNA double-strand breaks. To demonstrate this, we developed a humanized mouse model (hMPZL2Q74X/Q74X) that recapitulates human MPZL2 deafness and leads to progressive hearing loss. A PAM-flexible ABE variant with reduced bystander and off-target effects (ABE8eWQ-SpRY:sgRNA3) was packaged in dual adeno-associated viruses (AAVs) and injected into the inner ear of hMPZL2Q74X/Q74X mice and effectively corrected the mutation. This treatment significantly restored hearing function, improved inner ear structural integrity, and reversed altered gene expression. Base editing may hold therapeutic potential for hereditary deafness, including most cases of MPZL2 deafness.

genetics↗

bioRxiv2024

Polybacterial Intracellular Macromolecules Shape Single-Cell Epikine Profiles in Upper Airway Mucosa

The upper airway, particularly the nasal and oral mucosal epithelium, serves as a primary barrier for microbial interactions throughout life. Specialized niches like the anterior nares and the tooth are especially susceptible to dysbiosis and chronic inflammatory diseases. To investigate host-microbial interactions in mucosal epithelial cell types, we reanalyzed our single-cell RNA sequencing atlas of human oral mucosa, identifying polybacterial signatures (20% Gram-positive, 80% Gram-negative) within both epithelial- and stromal-resident cells. This analysis revealed unique responses of bacterial-associated epithelia when compared to two inflammatory disease states of mucosa. Single-cell RNA sequencing, in situ hybridization, and immunohistochemistry detected numerous persistent macromolecules from Gram-positive and Gram-negative bacteria within human oral keratinocytes (HOKs), including bacterial rRNA, mRNA and glycolipids. Epithelial cells with higher concentrations of 16S rRNA and glycolipids exhibited enhanced receptor-ligand signaling in vivo. HOKs with a spectrum of polybacterial intracellular macromolecular (PIM) concentrations were challenged with purified exogenous lipopolysaccharide, resulting in the synergistic upregulation of select innate (CXCL8, TNFSF15) and adaptive (CXCL17, CCL28) epikines. Notably, endogenous lipoteichoic acid, rather than lipopolysaccharide, directly correlated with epikine expression in vitro and in vivo. Application of the Drug2Cell algorithm to health and inflammatory disease data suggested altered drug efficacy predictions based on PIM detection. Our findings demonstrate that PIMs persist within mucosal epithelial cells at variable concentrations, linearly driving single-cell effector cytokine expression and influencing drug responses, underscoring the importance of understanding host-microbe interactions and the implications of PIMs on cell behavior in health and disease at single-cell resolution. One-sentence summaryThis study reveals how persistent intracellular bacterial macromolecules in mucosal epithelial cells drive inflammatory signaling, offering new insights into microbial-host interactions and their potential impact on inflammatory disease treatment and drug efficacy.

cell biology↗

bioRxiv2024

StrainR2 accurately deconvolutes strain-level abundances in synthetic microbial communities

BackgroundSynthetic microbial communities offer an opportunity to conduct reductionist research in tractable model systems. However, deriving abundances of highly related strains within these communities is currently unreliable. 16S rRNA gene sequencing does not resolve abundance at the strain level, standard methods for analysis of shotgun metagenomic sequencing do not account for ambiguous mapping between closely related strains, and other methods such as quantitative PCR (qPCR) scale poorly and are resource prohibitive for complex communities. We present StrainR2, which utilizes shotgun metagenomic sequencing paired with a k-mer-based normalization strategy to provide high accuracy strain-level abundances for all members of a synthetic community, provided their genomes. ResultsBoth in silico, and using sequencing data derived from gnotobiotic mice colonized with a synthetic fecal microbiota, StrainR2 resolves strain abundances with greater accuracy than other tools utilizing shotgun metagenomic sequencing reads and can resolve complex mixtures of highly related strains. Through experimental validation and benchmarking, we demonstrate that StrainR2s accuracy is comparable to that of qPCR on a subset of strains resolved using absolute quantification. Further, it is capable of scaling to communities of hundreds of strains and efficiently utilizes memory being capable of running both on personal computers and high-performance computing nodes. ConclusionsUsing shotgun metagenomic sequencing reads is a viable method for determining accurate strain-level abundances in synthetic communities using StrainR2.

bioinformatics↗

bioRxiv2023

Theranostic gold in a gold cage nanoparticle for photothermal ablation and photoacoustic imaging of skin and oral infections

AbstractBiofilms are structured communities of microbial cells embedded in a self-produced matrix of extracellular polymeric substances. Biofilms are associated with many health issues in humans, including chronic wound infections and tooth decay. Current antimicrobials are often incapable of disrupting the polymeric biofilm matrix and reaching the bacteria within. Alternative approaches are needed. Here, we describe a unique structure of dextran coated gold in a gold cage nanoparticle that enables photoacoustic and photothermal properties for biofilm detection and treatment. Activation of these nanoparticles with a near infrared laser can selectively detect and kill biofilm bacteria with precise spatial control and in a short timeframe. We observe a strong biocidal effect against both Streptococcus mutans and Staphylococcus aureus biofilms in mouse models of oral plaque and wound infections respectively. These effects were over 100 times greater than that seen with chlorhexidine, a conventional antimicrobial agent. Moreover, this approach did not adversely affect surrounding tissues. We conclude that photothermal ablation using theranostic nanoparticles is a rapid, precise, and non-toxic method to detect and treat biofilm-associated infections.

bioengineering↗

bioRxiv2020

Student-focused development of a next-generation centrifuge force microscope

Advanced biological molecule force probing methods such as atomic force microscopy and optical tweezers used to quantify forces at the single-molecule level are expensive and require extensive training and technical knowledge. However, the technologies underlying a centrifuge force microscope (CFM) are relatively straight forward, allowing for construction by labs with relatively low budgets and minimal training. Design ideas from previously constructed CFMs served as a guide in the development of this CFM. There were two primary goals: first, to develop an inexpensive, functional CFM using off-the-shelf and 3D printed parts; and second, to do so in the context of providing an educational experience for a broad range of students. The team included high school students and undergraduates from local high schools, the University of Minnesota, and other local higher education institutions. This project created an environment for student-focused development of the CFM that fostered active learning, individual ownership, as well as excellence in research. The instrument discussed herein represents a fully functional CFM designed and built by a postdoctoral researcher and a graduate student who together mentored several high school and undergraduate students. STATEMENT OF SIGNIFICANCEThe presented centrifuge force microscope (CFM) builds on features of existing designs specifically engineered for probing macromolecular force interactions at the single-molecule level. In the coming years, more versatile and modular CFM designs will be utilized in the force spectroscopy field, and the presented design is a step in that direction. In addition to constructing a functional instrument, true student ownership of the project design was equally an end goal. Students from high school through graduate school were included, and the project was structured so that everyone was seen as peers. This active learning project allowed students to acquire scientific concepts and techniques and apply them to real-life situations.

biophysics↗

bioRxiv2018

How cancer patients perceive clinical trials (CTs) in the era of CTs: Current perceptional status and differences between common and rare cancers

BackgroundAs perception have been recently highlighted as critical determinants of clinical trials (CTs) in cancer patients, we evaluated current perceptional status of CTs in cancer patients, focusing on differences between common and rare cancers.\n\nMaterials & MethodsFrom November 2015 to May 2017, we prospectively surveyed patients who have received anti-cancer treatment at Asan Medical Center using the PARTAKE questionnaires.\n\nResultsAmong 333 respondents, 70.9% and 29.1% had common and rare cancers, respectively. While 87.7% and 75.3% of patients answered that they heard of and knew about CTs, willingness to participate in CTs was expressed only in approximately 56% of patients although willingness was significantly correlated with awareness and perception. Surprisingly, patients with rare cancers showed significantly lower levels of awareness and perception (64.2% vs 79.9%, p=0.003 and 77.3% vs 91.9%, p<0.001), and consequently less willingness (47.4% vs 58.9%, p=0.06) compared to patients with common cancers. In addition, cancer patients still harbored fear with concerns about safety and reward, and substantial ignorance and mistrust about voluntariness of CTs, which was more predominant in patients with rare cancers.\n\nConclusionsPresent study identified relatively less willingness of CTs in cancer patients compared with generally favorable perception, and highlighted relative perceptional poverty in patients with rare cancers than those with common cancers. Further education and encouragement by research and public entities seem essential to raise motivation of CTs in cancer patients beyond good perception, especially for the patients with rare cancers.

epidemiology↗