Biology subjects

Kurabayashi, K.

Publications and source records attributed to Kurabayashi, K..

10 recordsLinked to original sources

bioRxiv2026

Patient-Derived Synovium-on-a-Chip Recapitulates Disease and Treatment Response and Permits Study of Resistance

Rheumatoid arthritis (RA) is a chronic inflammatory disease with substantial interpatient heterogeneity in synovial pathology and therapeutic response. Reliable methods to predict drug efficacy for a given patients remain a critical unmet need. We developed a vascularized, immunocompetent synovium-on-a-chip platform that integrates patient-derived fibroblast-like synoviocytes (FLS) with matched peripheral blood leukocytes to provide a physiological human model of RA. The platform reconstructed the lining-sublining synovial architecture, recapitulated key features of RA inflammation, and exhibited transcriptional profiles resembling those of patient synovial tissue. Across patients spanning low, mixed, and high inflammatory endotypes, stromal-vascular organization was associated with distinct immune cell positioning and activation patterns, and on-chip immune phenotypes correlated with histological joint inflammation scores. We then tested infliximab, tocilizumab, and tofacitinib in parallel and integrated cytokine secretion, extracellular matrix remodeling, immune cell survival and immune cell recruitment into a composite treatment response score. On-chip scores for clinically matched treatments correlated with clinical improvement measured by {Delta}DAS28-ESR (Pearson r = 0.844). To investigate the cellular basis of heterogeneous drug responses, single-cell RNA sequencing identified SFRP1 remodeling FLS that persisted under treatment and exhibited high inflammatory programs in poorly responding chips. Cell-cell communication analysis linked reduced FN1-CD44 signaling toward SFRP1 remodeling FLS to higher NF-{kappa}B activity and drug resistance. We tested the functional relevance of this finding in chips derived from an independent TNFi-nonresponsive patient, where fibronectin supplementation reduced IL-6 secretion and restored the composite treatment response. Together, these findings support patient-derived synovium-on-a-chip as a platform for individualized drug evaluation and identify ECM-mediated niche signaling as a potential therapeutic target for overcoming drug resistance in RA.

bioengineering↗

bioRxiv2025

Risk-Aware Control for Insulin Delivery via Nonlinear MPC with Safety Barrier Functions and Probabilistic Learning of Uncertainties

Maintaining blood glucose within a physiologically safe range is critical for people with diabetes, as deviations can lead to acute or chronic complications. Hypoglycemia, in particular, represents an immediate threat and requires prioritized mitigation in autonomous insulin delivery systems. This paper introduces a risk-aware hybrid nonlinear model predictive control (NMPC) framework that combines data-driven uncertainty quantification with formal safety assurance through control barrier functions (CBFs). To account for key uncertainties, such as physiological time delays, unannounced meals, and stress-induced glucose variability, Gaussian processes (GPs) are employed as probabilistic estimators. The proposed method dynamically monitors glucose and regulates insulin injection to enforce safe glucose level control by preventing hypoglycemia. The proposed framework is evaluated using validated physiological simulators for various realistic scenarios. The results show a robust performance in maintaining safety under high uncertainty, preparing a foundation for translation into next phase of our research as safe autonomous diabetes management systems.

bioengineering↗

bioRxiv2025

High Spatiotemporal Imaging of Protein Secretion During Cell to Cell Communication via Integrative Biosensing Nanoplasmonic Array

Protein secretion underpins diverse physiological processes in cell-to-cell communication, tissue homeostasis, and the onset of diseases. Mapping the secretomes from paired cells provides avenues for understanding their interactions. However, prevailing approaches yield only semi-quantitative endpoint data, lacking real-time and quantitative information. Here, we present real time spatiotemporal imaging of extracellular secretions from individual cells via a high-throughput integrative biosensing nanoplasmonic array (iBNA) with a microfluidic chamber. The self-assembled iBNA, composed of precisely arranged gold nanostructures and functionalized with aptamer receptors, enhances plasmonic resonance and significantly improves the spatiotemporal resolution and specificity of interleukin-6 (IL-6) imaging, surpassing gold-standard techniques. The molecular recognition of iBNA, and sensing mechanism exploits biomolecular surface binding-induced localized plasmonic resonance shifts, correlating with cytokine concentration and enabling optoelectronic detection of the transmitted light. Using this approach, we achieve spatiotemporally resolved visualization of IL-6 secretion dynamics at the single-cell level and unveil the temporal and polarized variation of cell-cell communications. This transformative platform holds significant potential to advance immunological research, cellular biology, and diagnostic applications for infectious diseases by enabling unprecedented insights into the spatiotemporal patterns of protein secretion in individual cells.

bioengineering↗

bioRxiv2025

High-temporal-resolution point-of-care multiplex biomarker monitoring in small animals using microfluidic digital ELISA

Time-course monitoring of blood biomarkers with rapid turnaround has the potential to revolutionize the diagnosis, stratification of phenotypes, and therapeutic/prognostic approaches for various acute inflammatory diseases in both clinical and preclinical studies. Current approaches, however, are hampered by slow turnaround times and large sample volume requirements, limiting the exploration of disease mechanisms and therapeutic strategies. Here, we developed a microfluidic digital ELISA platform prototype, combining single-molecule counting with whole blood assay capability for the first time from small animal models. This platform is automated and enables repeated, rapid biomarker monitoring with just 3.5 {micro}L of whole blood collected from the tail. Our platform demonstrated high sensitivity and multiplexity, allowing real-time cytokine profiling within a 2-hour turnaround. Using a murine sepsis model, we achieved precise temporal monitoring of cytokine levels, demonstrating prognostic capability by correlating early-stage cytokine levels with a liver-injury biomarker. This microfluidic platform enables high temporal resolution and rapid monitoring of biomarker dynamics in a single mouse using freshly collected whole blood, significantly reducing the number of animals needed for preclinical studies. This technology has strong potential to transform ICU therapeutic strategies and preclinical research, enabling personalized treatment based on real-time biomarker profiles.

bioengineering↗

bioRxiv2024

Sustaining microglial reparative function enhances stroke recovery

Neurological symptoms after brain injury can remain as lifelong detrimental sequelae since most spontaneous brain recovery disappears within a few months after brain injury. Microglia play an essential role in recovery processes after brain injury; however, cellular and molecular mechanisms that diminish spontaneous brain functional recovery remain unknown. We discovered by cellular fate analysis that reparative myeloid cells remained in the post-stroke brain even after losing their reparative function. ZFP384 was identified as a pivotal transcriptional regulator that diminished recovery phase-associated gene expression in reparative myeloid cells, turning them into ruined cells which lost reparative functions. ZFP384 diminished the YY1-mediated chromatin interaction necessary for expressing recovery phase-associated genes. Antisense oligonucleotide against Zfp384 sustained the broad range of neural repair effects of myeloid cells and enhanced stroke recovery, even in the chronic phase of ischemic stroke recovery. Thus, therapeutics preventing the myeloid reparative immunity from reaching a ruined state sustains brain functional recovery.

pathology↗

bioRxiv2022

The Modular μSiM: a Mass Produced, Rapidly Assembled, and Reconfigurable Platform for the Study of Barrier Tissue Models In Vitro

Advanced in vitro tissue chip models can reduce and replace animal experimentation and may eventually support on-chip clinical trials. To realize this potential, however, tissue chip platforms must be both mass-produced and reconfigurable to allow for customized design. To address these unmet needs, we introduce an extension of our {micro}SiM (microdevice featuring a silicon-nitride membrane) platform. The modular {micro}SiM (m-{micro}SiM) uses mass-produced components to enable rapid assembly and reconfiguration by laboratories without knowledge of microfabrication. We demonstrate the utility of the m-{micro}SiM by establishing an hiPSC-derived blood-brain barrier (BBB) in bioengineering and non-engineering, brain barriers focused laboratories. We develop and validate in situ and sampling-based assays of small molecule diffusion as a measure of barrier function. BBB properties show excellent interlaboratory agreement and match expectations from literature, validating the m-{micro}SiM as a platform for barrier models and demonstrating successful dissemination of components and protocols. We then demonstrate the ability to quickly reconfigure the m-{micro}SiM for co-culture and immune cell transmigration studies through addition of accessories and/or quick exchange of components. Because the development of modified components and accessories is easily achieved, custom designs of the m-{micro}SiM should be accessible to any laboratory desiring a barrier-style tissue chip platform.

bioengineering↗

bioRxiv2020

Extracellular DJ-1 induces sterile inflammation in the ischemic brain

Inflammation is implicated in the onset and progression of various diseases, including cerebral pathologies. Here we report that DJ-1, which plays a role within cells as an antioxidant protein, functions as a damage-associated molecular pattern (DAMP), and triggers inflammation if released from dead cells into the extracellular space. We first found that recombinant DJ-1 protein induces the production of various inflammatory cytokines in bone marrow-derived macrophages (BMMs). We further identified a unique peptide sequence in the G and H helices of DJ-1 that activates Toll-like receptor 2 (TLR2) and TLR4. In the ischemic brain, DJ-1 is released into the extracellular space from necrotic neurons within 24 hours after stroke onset and makes direct contact with the surfaces of infiltrating myeloid cells. Administration of an antibody against DJ-1 suppresses the expression of inflammatory cytokines in infiltrating immune cells and attenuates ischemic neuronal damage. Our results demonstrate a previously unknown function of DJ-1 as a DAMP and suggest that extracellular DJ-1 could be a therapeutic target to prevent inflammation in tissue injuries and neurodegenerative diseases. Significance statementDJ-1 has been thoroughly investigated as a cytoprotective antioxidant protein in neurons. However, here we demonstrate that extracellularly released DJ-1 triggers neurotoxic inflammation after ischemic stroke. Intracellular DJ-1 increases in response to oxidative stress in ischemic neurons, but if ischemic stresses result in necrotic cell death, DJ-1 is released extracellularly. Released DJ-1 interacts with TLR2 and TLR4 on the surface of infiltrating myeloid cells and triggers post-ischemic inflammation, leading to the exacerbated pathologies of ischemic stroke. Thus, extracellular DJ-1 is a previously unknown inflammatogenic DAMP, and may be a putative target for therapeutic intervention to prevent progression of inflammatory and neurodegenerative diseases.

immunology↗

bioRxiv2020

Machine Learning-Based Protein Microarray Digital Assay Analysis

Serial measurement of a large panel of protein biomarkers near the bedside could provide a promising pathway to transform the critical care of acutely ill patients. However, attaining the combination of high sensitivity and multiplexity with a short assay turnaround poses a formidable technological challenge. Here, we developed a rapid, accurate, and highly multiplexed microfluidic digital immunoassay by incorporating machine learning-based autonomous image analysis. The assay achieved 14-plexed biomarker detection at concentrations < 10pg/mL with a sample volume < 10 L, including all processes from sampling to analyzed data delivery within 30 min, while only requiring a 5-min assay incubation. The assay procedure applied both a spatial-spectral microfluidic encoding scheme and an image data analysis algorithm based on machine learning with a convolutional neural network (CNN) for pre-equilibrated single-molecule protein digital counting. This unique approach remarkably reduced errors facing the high-capacity multiplexing of digital immunoassay at low protein concentrations. Longitudinal data obtained for a panel of 14 serum cytokines in human patients receiving chimeric antigen receptor-T (CAR-T) cell therapy manifested the powerful biomarker profiling capability and great potential of the assay for its translation to near-real-time bedside immune status monitoring.

bioengineering↗

bioRxiv2020

Optimized gene expression from bacterial chromosome by high-throughput integration and screening

Chromosomal integration of recombinant genes is desirable compared to expression from plasmids due to increased stability, reduced cell-to-cell variability, and the elimination of antibiotics for plasmid maintenance. Here, we present a new approach for tuning pathway gene expression levels via random integrations and high-throughput screening. We demonstrate multiplexed gene integration and expression-level optimization for isobutanol production in Escherichia coli. The integrated strains could, with significantly lower expression levels than plasmid-based expression, produce high titers (10.0 {+/-} 0.9 g/L isobutanol in 48 h) and yields (69 % of the theoretical maximum). Close examination of pathway expression in the top-performing, as well as other isolates, reveals the complexity of cellular metabolism and regulation, underscoring the need for precise optimization while integrating pathway genes into the chromosome. This new method for multiplexed pathway gene integration and expression optimization could be readily extended to a wide range of pathways and chassis to create robust and efficient production strains.

synthetic biology↗

bioRxiv2019

Syntrophic co-culture amplification of production phenotype for high-throughput screening of microbial strain libraries

Microbes can be engineered to synthesize a wide array of bioproducts, yet production phenotype evaluation remains a frequent bottleneck in the design-build-test cycle where strain development requires iterative rounds of library construction and testing. Here, we present Syntrophic Co-culture Amplification of Production phenotype (SnoCAP). Through a metabolic cross-feeding circuit, the production level of a target molecule is translated into highly distinguishable co-culture growth characteristics, which amplifies differences in production into highly distinguishable growth phenotypes. We demonstrate SnoCAP with the screening of Escherichia coli strains for production of two target molecules: 2-ketoisovalerate, a precursor of the drop-in biofuel isobutanol, and L-tryptophan. The dynamic range of the screening can be tuned by employing an inhibitory analog of the target molecule. Screening based on this framework requires compartmentalization of individual producers with the sensor strain. We explore three formats of implementation with increasing throughput capability: confinement in microtiter plates (102-104 assays/experiment), spatial separation on agar plates (104-105 assays/experiment), and encapsulation in microdroplets (105-107 assays/experiment). Using SnoCAP, we identified an efficient isobutanol production strain from a random mutagenesis library, reaching a final titer that is 5-fold higher than that of the parent strain. The framework can also be extended to screening for secondary metabolite production using a push-pull strategy. We expect that SnoCAP can be readily adapted to the screening of various microbial species, to improve production of a wide range of target molecules.

synthetic biology↗