Biology subjects

Yu, J. S.

Publications and source records attributed to Yu, J. S..

13 recordsLinked to original sources

bioRxiv2026

3D Printed Bioelectronic Scaffolds for Impedance-based Cytotoxicity Monitoring of In Vitro Cancer Models

Cancer is a significant contributor to global mortality and places a substantial burden on healthcare systems, underscoring the need for improved strategies for developing and evaluating new therapies. Electrochemical impedance monitoring of in vitro cancer models is a promising technique for evaluating treatment effectiveness, particularly for evaluating how well a drug may kill cancer cells. This approach is advantageous over conventional end-point assays because it is non-destructive, label-free, and can provide temporal information on cell behavior and drug kinetics. However, traditional impedance devices are limited in that they do not support three-dimensional cell culture that has become standard in cancer studies. Typical devices are planar substrates that support monolayer culture, which has been shown to overestimate drug effectiveness. In this work, we propose 3D printed bioelectronic scaffold devices that provide 3D cancer cell culture while functioning as an on-chip readout for monitoring changes in cell characteristics via impedance. We describe device development and demonstrate reproducible fabrication, stable electrochemical properties, cell detection by impedance, and proof-of-concept monitoring of cytotoxicity in response to a chemotherapeutic drug. Overall, this technology offers a promising platform that could be further developed for compound screening as part of drug development or precision medicine.

bioengineering↗

bioRxiv2026

Additive manufacturing of PEDOT:PSS electrodes on collagen substrates for soft and bioactive electronics

Traditional bioelectronic devices are limited by poor biointerfacing due to their substantial mismatch in mechanical and biochemical properties. In tissue engineering, soft and bioactive materials support biointegration by harnessing or mimicking the natural extracellular matrix (ECM). Building bioelectronic devices from ECM should improve their biointegration, yet there are limited methods to fabricate them due to current manufacturing approaches. An additive manufacturing strategy is presented here for collagen-based bioelectronic interfaces that integrates conducting polymer electrodes with ECM-based substrates or encapsulation layers. Addition of poly(ethylene glycol) diglycidyl ether (PEGDE) to poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) colloidal dispersions enables direct extrusion-based patterning under mild conditions compatible with collagen substrates, and forms aqueous stable and highly conducting printed patterns (2788 S m-{superscript 1}). The resulting interfaces maintain stable electrochemical performance over 7 days in physiological environments, and support primary human cell adhesion, viability, and proliferation across both material regions. A sacrificial patterning strategy using 3D printed cacao butter further enables spatial control of collagen encapsulation. This approach establishes a framework for fabricating functional bioelectronic devices based on ECM to further enhance device biointerfaces for tissue models and implantable systems.

bioengineering↗

bioRxiv2025

PEDOT:PSS Microparticles for Extrudable and Bioencapsulating Conducting Granular Hydrogel Bioelectronics

Conducting hydrogels are promising materials for forming physiomimetic bioelectronic interfaces to monitor and stimulate biological activity. However, most developed materials are non-microporous and possess fixed shapes, both of which can limit the integration of cells and tissues with devices. In non-conducting biomaterials, materials fabrication strategies imparting microporosity and dynamic mechanical properties have been shown to support cell infiltration and support biointerfaces of various geometries. Specifically, granular hydrogels have enabled encapsulating, conformal, and injectable interfaces through these features. However, granular hydrogels remain largely unexplored as conducting biomaterials. We present methods for fabricating spherical, poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) hydrogel microparticles. When densely packed, these microparticles form a conducting granular hydrogel with microporosity as well as shear-thinning and self-healing dynamic mechanical properties. The PEDOT:PSS granular hydrogel can be extruded and maintain structure post-3D printing. Modulating microparticle PSS content achieves high granular hydrogel conductivity (137 S/m), and microparticles exhibit excellent cytocompatibility (>98% viability). Finally, we demonstrate utility as bioencapsulating electrodes for electrophysiological monitoring. These results highlight the functionality of our PEDOT:PSS conducting granular hydrogel, suggesting its potential as 3D printed bioencapsulating electrodes, 3D tissue engineering scaffolds for monitoring encapsulated cells, and injectable therapies for enhanced cell recruitment and tissue regeneration combined with electronic stimulation.

bioengineering↗

bioRxiv2024

4D hybrid model interrogates agent-level rules and parameters driving hiPS cell colony dynamics

Iterating between data-driven research and generative computational models is a powerful approach for emulating biological systems, testing hypotheses, and gaining a deeper understanding of these systems. We developed a hybrid agent-based model (ABM) that integrates a Cellular Potts Model (CPM) designed to investigate cell shape and colony dynamics in human induced pluripotent stem cell (hiPS cell) colonies. This model aimed to first mimic and then explore the dynamics observed in real-world hiPS cell cultures. Initial outputs showed great potential, seeming to mimic small colony behaviors relatively well. However, longer simulations and quantitative comparisons revealed limitations, particularly with the CPM component, which lacked long-range interactions that might be necessary for accurate simulations. This challenge led us to thoroughly examine the hybrid models potential and limitations, providing insights and recommendations for systems where cell-wide mechanics play significant roles. The CPM supports 2D and 3D cell shapes using a Monte Carlo algorithm to prevent cell fragmentation. Basic "out of the box" CPM Hamiltonian terms of volume and adhesion were insufficient to match live cell imaging of hiPS cell cultures. Adding substrate adhesion resulted in flatter colonies, highlighting the need to consider environmental context in modeling. High-throughput parameter sweeps identified regimes that produced consistent simulated shapes and demonstrated the impact of specific model decisions on emergent dynamics. Full-scale simulations showed that while certain agent rules could form a hiPS cell monolayer in 3D, they could not maintain it over time. Our study underscores that "out of the box" 3D CPMs, which do not natively incorporate long-range cell mechanics like elasticity, may be insufficient for accurately simulating hiPS cell and colony dynamics. To address this limitation, future work could add mechanical constraints to the CPM Hamiltonian or integrate global agent rules. Alternatively, replacing the CPM with a methodology that directly represents cell mechanics might be necessary. Documenting and sharing our model development process fosters open team science and supports the broader research community in developing computational models of complex biological systems.

systems biology↗

bioRxiv2024

3D printed bioelectronic scaffolds with soft tissue-like stiffness

3D printing is a leading technique for fabricating tissue engineering scaffolds that facilitate native cellular behavior. Engineering scaffolds to possess functional properties like electronic conductivity is the first step towards integrating new technological capabilities like stimulating or monitoring cellular activity beyond the traditionally presented biophysical and biochemical cues. However, these bioelectronic scaffolds have been largely underdeveloped since the majority of electrically conducting materials possess high stiffness values outside the physiological range and that may negatively impact desired cell behavior. Here, we present methods of 3D printing poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) hydrogel scaffolds and provide techniques to achieve stiffness relevant to many soft tissues (<100 kPa). Structures were confirmed as ideal tissue scaffolds by maintaining biostability and promoting high cell viability, appropriate cell morphology, and proliferation. With these findings, we contribute a customizable 3D platform that provides favorable soft cellular microenvironments and envision it to be adaptable to several bioelectronic applications.

bioengineering↗

bioRxiv2024

Incorporating temporal information during featureengineering bolsters emulation of spatio-temporalemergence

MotivationEmergent biological dynamics derive from the evolution of lower-level spatial and temporal processes. A long-standing challenge for scientists and engineers is identifying simple low-level rules that give rise to complex higher-level dynamics. High-resolution biological data acquisition enables this identification and has evolved at a rapid pace for both experimental and computational approaches. Simultaneously harnessing the resolution and managing the expense of emerging technologies--e.g. live cell imaging, scRNAseq, agent-based models--requires a deeper understanding of how spatial and temporal axes impact biological systems. Effective emulation is a promising solution to manage the expense of increasingly complex high-resolution computational models. In this research, we focus on the emulation of a tumor microenvironment agent-based model to examine the relationship between spatial and temporal environment features, and emergent tumor properties. ResultsDespite significant feature engineering, we find limited predictive capacity of tumor properties from initial system representations. However, incorporating temporal information derived from intermediate simulation states dramatically improves the predictive performance of machine learning models. We train a deep-learning emulator on intermediate simulation states and observe promising enhancements over emulators trained solely on initial conditions. Our results underscore the importance of incorporating temporal information in the evaluation of spatio-temporal emergent behavior. Nevertheless, the emulators exhibit inconsistent performance, suggesting that the underlying model characterizes unique cell populations dynamics that are not easily replaced. AvailabilityAll source codes for the agent-based model, emulation, and analyses are publicly available at github.com/bagherilab/ARCADE, github.com/bagherilab/emulation, and github.com/bagherilab/emulation_analysis, respectively. Contactnbagheri@uw.edu

systems biology↗

bioRxiv2023

Tumor cell-derived spermidine promotes a pro-tumorigenic immune microenvironment in glioblastoma via CD8+ T cell inhibition

The glioblastoma microenvironment is enriched in immunosuppressive factors that potently interfere with the function of cytotoxic T lymphocytes. Cancer cells can directly impact the immune system, but the mechanisms driving these interactions are not completely clear. Here we demonstrate that the polyamine metabolite spermidine is elevated in the glioblastoma tumor microenvironment. Exogenous administration of spermidine drives tumor aggressiveness in an immune-dependent manner in pre-clinical mouse models via reduction of CD8+ T cell frequency and phenotype. Knockdown of ornithine decarboxylase, the rate-limiting enzyme in spermidine synthesis, did not impact cancer cell growth in vitro but did result in extended survival. Furthermore, glioblastoma patients with a more favorable outcome had a significant reduction in spermidine compared to patients with a poor prognosis. Our results demonstrate that spermidine functions as a cancer cell-derived metabolite that drives tumor progression by reducing CD8+T cell number and function.

cancer biology↗

bioRxiv2023

Serum amyloid A-dependent inflammasome activation and acute injury in a mouse model of experimental stroke

BACKGROUNDSerum amyloid A (SAA) proteins increase dramatically in the blood following inflammation. Recently, SAAs are increased in humans following stroke and in ischemic animal models. However, the impact of SAAs on whether this signal is critical in the ischemic brain remains unknown. Therefore, we investigated the role of SAA and SAA signaling in the ischemic brain. METHODSWildtype and SAA deficient mice were exposed to middle cerebral artery occlusion and reperfusion, examined for the impact of infarct volumes, behavioral changes, inflammatory markers, TUNEL staining, and BBB changes. The underlying mechanisms were investigated using SAA deficient mice, transgenic mice and viral vectors. RESULTSSAA levels were significantly increase following MCAo and mice deficient in SAAs showed reduced infarct volumes and improved behavioral outcomes. SAA deficient mice showed a reduction in TUNEL staining, inflammation and decreased glial activation. Mice lacking acute phase SAAs demonstrated a reduction in expression of the NLRP3 inflammasome and SAA/NLRP3 KO mice showed improvement. Restoration of SAA expression via SAA tg mice or adenoviral expression reestablished the detrimental effects of SAA. A reduction in BBB permeability was seen in the SAA KO mice and anti-SAA antibody treatment reduced the effects on ischemic injury. CONCLUSIONSSAA signaling plays a critical role in regulating NLRP3-induced inflammation and glial activation in the ischemic brain. Blocking this signal will be a promising approach for treating ischemic stroke. GRAPHIC ABSTRACTA graphic abstract is available for this article.

neuroscience↗

bioRxiv2022

Mapping CAR T-cell design space using agent-based models

Chimeric antigen receptor (CAR) T-cell therapy shows promise for treating liquid cancers and increasingly for solid tumors as well. While potential design strategies exist to address translational challenges, including the lack of unique tumor antigens and the presence of an immunosuppressive tumor microenvironment, testing all possible design choices in vitro and in vivo is prohibitively expensive, time consuming, and laborious. To address this gap, we extended the modeling framework ARCADE (Agent-based Representation of Cells And Dynamic Environments) to include CAR T-cell agents (CAR T-cell ARCADE, or CARCADE). We conducted in silico experiments to investigate how clinically relevant design choices and inherent tumor features--CAR T-cell dose, CD4+:CD8+ CAR T-cell ratio, CAR-antigen affinity, cancer and healthy cell antigen expression--individually and collectively impact treatment outcomes. Our analysis revealed that tuning CAR affinity modulates IL-2 production by balancing CAR T-cell proliferation and effector function. It also identified a novel multi-feature tuned treatment strategy for balancing selectivity and efficacy and provided insights into how spatial effects can impact relative treatment performance in different contexts. CARCADE facilitates deeper biological understanding of treatment design and could ultimately enable identification of promising treatment strategies to accelerate solid tumor CAR T-cell design-build-test cycles.

bioengineering↗

bioRxiv2022

Inorganic sulfur fixation via a new homocysteine synthase allows yeast cells to cooperatively compensate for methionine auxotrophy

The assimilation, incorporation, and metabolism of sulfur is a fundamental process across all domains of life, yet how cells deal with varying sulfur availability is not well understood. We studied an unresolved conundrum of sulfur fixation in yeast, in which an organosulfur-auxotrophy caused by deletion of homocysteine synthase Met17p is overcome when cells are inoculated at high cell density. We discovered that an uncharacterized gene YLL058Wp, herein named Hydrogen sulfide utilizing-1 (HSU1), acts as a homocysteine synthase and allows the cells to substitute for Met17p by re-assimilating hydrosulfide ions leaked from met17{Delta} cells into O-acetyl-homoserine and forming homocysteine. Our results show that cells can cooperate to achieve sulfur fixation, indicating that the collective properties of microbial communities facilitate their basic metabolic capacity. SummarySulfur limitation activates a dormant hydrogen sulfide fixation route via a novel homocysteine synthase Hsu1p (YLL058Wp).

molecular biology↗

bioRxiv2021

HAUSP Stabilizes SOX2 through Deubiquitination to Maintain Self-renewal and Tumorigenic Potential of Glioma Stem Cells

Glioblastoma (GBM) is the most lethal brain tumor containing glioma stem cells (GSCs) that promote malignant growth and therapeutic resistance. The self-renewal and tumorigenic potential of GSCs are maintained by core stem cell transcription factors including SOX2. Defining the posttranslational regulation of SOX2 may offer new insights into GSC biology and potential therapeutic opportunity. Here, we discover that HAUSP stabilizes SOX2 through deubiquitination to maintain GSC self-renewal and tumorigenic potential. HAUSP is preferentially expressed in GSCs in perivascular niches in GBMs. Disrupting HAUSP by shRNA or its inhibitor P22077 promoted SOX2 degradation, induced GSC differentiation, impaired GSC tumorigenic potential, and suppressed GBM tumor growth. Importantly, pharmacological inhibition of HAUSP synergized with radiation to inhibit GBM growth and extended animal survival, indicating that targeting HAUSP may overcome GSC-mediated radioresistance. Our findings reveal an unappreciated crucial role of HAUSP in the GSC maintenance and provide a promising target for developing effective anti-GSC therapeutics to improve GBM treatment. HighlightsO_LIHAUSP deubiquitinates and stabilizes SOX2 in glioma stem cells (GSCs). C_LIO_LIHAUSP is preferentially expressed by GSCs in perivascular niches in GBMs. C_LIO_LIHAUSP is required for maintaining GSC self-renewal and tumorigenic potential. C_LIO_LITargeting HAUSP inhibited malignant growth in GSC-derived GBM xenografts. C_LIO_LIInhibition of HAUSP synergized with radiation to suppress GBM tumor growth. C_LI

cancer biology↗

bioRxiv2021

A Novel Non-Invasive Epithelial Ovarian Cancer Mouse Model Of Hyperthermic Intraperitoneal Chemotherapy (HIPEC)

BackgroundHyperthermic intraperitoneal chemotherapy (HIPEC) in combination with interval cytoreductive surgery increases the overall survival of epithelial ovarian cancer (EOC) patients with advanced disease. Despite its proven benefits, the mechanism by which HIPEC extends overall survival remains unknown and current strategies to optimize HIPEC are therefore limited. A major challenge is the lack of a robust and streamlined model to investigate the mechanisms underlying HIPEC efficacy. ObjectiveTo introduce a novel murine model that can be used to enhance our understanding of HIPEC therapy. MethodID8-luc, an EOC mouse cell line, is inoculated into immunocompetent C57BL/6J mice intraperitoneally. Once tumor is detected by In Vivo Imaging System (IVIS), cisplatin (5 mg/kg) is injected intraperitoneally and superficial hyperthermia of 40{degrees}C is applied to the animals abdomen and pelvis using an FDA-approved hyperthermia unit (BSD500) for 20 minutes. To validate the model, four treatment conditions were tested: cisplatin and hyperthermia, cisplatin and normothermia, vehicle and hyperthermia, and vehicle and normothermia. Tumor growth was assessed over the course of treatment using IVIS optical spectrum. ResultsTumor growth in mice treated with hyperthermic cisplatin was significantly suppressed compared to mice treated with normothermic cisplatin (p < 0.05). No significant differences in tumor growth were observed in the hyperthermic vehicle and normothermic vehicle groups. ConclusionsWe developed an innovative noninvasive mouse model of HIPEC. Similar to patients with advanced ovarian cancer who are treated with HIPEC at the time of interval cytoreductive surgery, our model demonstrates that hyperthermia enhances the inhibitory effect of cisplatin on intraperitoneal tumor growth. Development of this murine model provides an opportunity to elucidate the mechanisms underlying HIPEC and offer an opportunity to test adjunct treatments in a pre-clinical setting to enhance the utility of HIPEC.

cancer biology↗

bioRxiv2021

Resolving the Interactions Between Class 3 Semaphorin Receptors in Live Cells

The plexin/neuropilin/semaphorin family of proteins is involved with tissue patterning in the developing embryo. These proteins play roles in cell migration and adhesion, but are also important in disease, including cancer angiogenesis and metastasis. While some structures of the soluble domains of these proteins have been determined, the conformations of full-length receptor complexes are just beginning to be studied, especially within the context of the cell plasma membrane. Pulsed-interleaved excitation fluorescence cross-correlation spectroscopy (PIE-FCCS) allows direct insight to the formation of protein-protein interactions in the membrane of live cells. Here we investigated the homodimerization of neuropilin-1, Plexin A2, Plexin A4, and Plexin D1. Consistent with previous studies, we found that neuropilin-1, Plexin A2 and Plexin A4 are dimers in the absence of exogenous ligand. Plexin D1, on the other hand, was monomeric under similar conditions, which had not been previously reported. We also found that Plexin A2 and A4 assemble into a heteromeric complex. Stimulation with Semaphorin 3A or Semaphorin 3C ligand neither disrupts nor enhances the dimerization of the receptors when they are expressed alone, suggesting that activation involves a conformational change rather than a shift in the monomer-dimer equilibrium. However, upon stimulation with Semaphorin 3C, Plexin D1 and neuropilin-1 form a heteromeric complex, while Semaphorin 3A does not induce a stable complex with these receptors. This analysis of interactions by PIE-FCCS provides a complementary approach to the existing structural and biochemical data that will aid in the development of new therapeutic strategies to target these receptors during disease.

biophysics↗