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APL Bioengineering

AIP Publishing

Preprints posted in the last 90 days, ranked by how well they match APL Bioengineering's content profile, based on 19 papers previously published here. The average preprint has a 0.01% match score for this journal, so anything above that is already an above-average fit.

1
Microfluidic Platform for Drug Response Profiling in NSCLC Patient-Derived Organoids

Luan, Q.; Rahnama, A.; Pulido, I.; Raspini, M.; Zhou, J.; Shimamura, T.; Papautsky, I.

2026-06-19 bioengineering 10.64898/2026.06.17.733025 medRxiv
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Tumor models that recapitulate 3D architecture are essential for understanding how cellular organization and microenvironmental interactions govern therapeutic response in human cancers. Here, we developed a microfluidic microphysiological system that enables controlled and scalable culture and drug testing of non-small cell lung cancer spheroids and patient-derived organoids. The platform integrated U-shaped microwells with dual-channel loading to support de novo spheroid formation, efficient trapping of pre-formed spheroids, and loading of intact organoids with reduced size heterogeneity. Tumor spheroids and organoids maintained high viability and structural integrity during long-term on-chip culture, and constrained microscale confinement produced ellipsoidal geometries that deviate from idealized spherical assumptions. Baseline genotype-dependent responses to KRAS G12C and EGFR inhibitors were preserved across agarose and microfluidic formats, establishing a validated reference state. Building on this baseline, fibroblast- and endothelial-derived cues consistently attenuated responses to targeted therapies across conditioned media, mixed co-culture, and spatially organized configurations. Resistance phenotypes converged on a dominant role for paracrine signaling, while increasing architectural complexity primarily enhanced morphological fidelity rather than altering therapeutic response. These findings establish a microphysiological framework that decouples tumor-intrinsic drug sensitivity from microenvironment-mediated modulation, enabling the systematic evaluation of paracrine resistance mechanisms in NSCLC.

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Tumor-Associated EDA-FN-Enriched Matrix Instructs Macrophage Behavior

Bashiri, G.; Bakare, E.; Longstreth, J.; Padilla, M.; Wang, K.

2026-05-18 bioengineering 10.64898/2026.05.14.725237 medRxiv
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IntroductionCancer progression is driven not only by tumor cells but also by interactions between the extracellular matrix (ECM), stromal cells, and immune cells within the tumor microenvironment (TME). Cancer-associated fibroblasts (CAFs) are major drivers of ECM remodeling, assembling ECM with aberrant organization. Extra domain A fibronectin (EDA-FN), a cellular FN containing an extra type III domain, is upregulated in the TME. EDA-FN regulates cellular behavior and has been associated with poor patient prognosis. Macrophages are among the most abundant immune cells within the TME, where they contribute to TME remodeling and inflammation to promote cancer cell invasion and metastasis. However, how tumor-associated matrix-specific cues regulate macrophage behavior remains largely understudied. PurposeHere, we developed a fibroblast-derived matrix platform that captures the structural imprint of tumor-associated EDA-enriched matrices and investigated how matrix-specific cues regulate macrophage behavior in the absence of ongoing soluble factor cues. MethodHuman mammary fibroblasts (HMFs) preconditioned in incubated low-serum media (lNC, or control) and MDA-MB231 metastatic breast cancer cell-conditioned media (mTCM) were cultured on polyacrylamide gels of 2 kPa and 20 kPa, respectively, followed by decellularization. Matrix organization, including fiber alignment, width, and intrafibrillar spacing, was quantified from confocal images. Decellularized EDA-FN-enriched matrices were subsequently reseeded with macrophages to assess macrophage morphology, phenotype, and matrix interactions. ResultsThe combined effects of tumor-derived soluble factors and pathological stiffness induced a CAF-like phenotype in HMFs, accompanied by cytoskeletal reorganization and microarchitectural alterations of EDA-FN-enriched matrices. Tumor-associated matrices exhibited increased alignment, narrower fiber width, and enlarged intrafibrillar spacing compared to control matrices. These aberrant, tumor-associated matrix-derived features were associated with altered macrophage behavior, including heterogeneous morphology, enhanced localized EDA-FN matrix loss beneath the cell body, and a hybrid phenotype with a shift toward a CD206-dominant profile. ConclusionsThese findings demonstrate the feasibility of obtaining EDA-FN-enriched matrices to isolate matrix-specific cues for investigating macrophage-ECM interactions. Furthermore, this platform can be leveraged to identify matrix-targeting therapeutic approaches for modulating macrophage function within the TME.

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Magnetoactive hydrogels to probe curvature-directed endothelial cell mechanosensing

Loebel, C.; Roy, A.; Hinds, G. K.; Liu, J. Y.-C.; Yanala, R.; Velieva, A.

2026-05-07 bioengineering 10.64898/2026.05.04.722723 medRxiv
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The vascular system exhibits complex, non-planar geometries that become further distorted during pathological remodeling, including arterial tortuosity and aneurysms. Although hemodynamic shear stress is a well-established regulator of vascular function, the direct effects of curvature as an intrinsic geometric cue remain poorly defined. This is largely because existing in vitro models are static and fail to capture the dynamic changes that accompany disease progression. To address this gap, we used a magnetoactive hydrogel platform that enables real-time, on-demand curvature of endothelial monolayers to reproduce clinically established tortuosity metrics. Using this system, we found that elevated curvature increased nuclear localization of yes-associated protein (YAP), with the strongest response in convex relative to concave regions of highly tortuous endothelial monolayers. This mechanosensitive response was accompanied by reduced VE-Cadherin junctional thickness and increased membrane localization of endothelial nitric oxide synthase. Together, these findings identify local curvature, independent of shear stress, as a regulator of endothelial cell mechanosensing and function, and establish a dynamic hydrogel platform for isolating geometric regulation from shear stress inputs in vascular mechanobiology.

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A confining microfluidic platform for disparate density coculture reveals the dynamics of macrophage-mediated adipocyte clearance

Lim, Y. B.; Kabigting, J. E.; Cheam, M. S.; Toyama, Y.; Holle, A.

2026-05-21 bioengineering 10.64898/2026.05.19.726422 medRxiv
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Co-culturing cells with mismatched densities, where one cell type adheres to surfaces while the other floats, represents a fundamental challenge in cell biology. This is particularly evident in studying macrophage-adipocyte interactions, where macrophages must engage and clear lipid-rich apoptotic adipocytes, a process critical to understanding chronic inflammation in obesity and metabolic disease. The density disparity between macrophages, which sink and adhere to culture surfaces, and adipocytes, which float due to their lipid content, has prevented conventional co-culture approaches from achieving sustained cell-cell contact. To address this challenge, we developed a microfluidic system that confines adipocytes and lipid droplets in close proximity to macrophages. This platform features recessed micro-traps within the upper surface of a microfluidic chamber that trap buoyant objects while allowing media exchange and delivery of reagents for live-cell and immunofluorescence imaging. Time lapse imaging revealed that the dynamic process of macrophages-dead corpse interactions, showing that individual macrophages cannot engulf entire corpses but instead mechanically deform them. Furthermore, the platform successfully recapitulates the formation of Crown-Like Structures (CLS), clusters of macrophages surrounding dead adipocytes that are hallmarks of adipose tissue inflammation. Long-term culture revealed that CLS effectively clear lipids compared to partial macrophage engagement, providing mechanistic insights that were previously unattainable with standard histological approaches. Beyond the macrophage-lipid interaction, this platform has potential for studying interactions between adherent cells and buoyant targets, such as microplastics, opening new avenues for research where density mismatch poses a major barrier.

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Organ on chip model of respiratory vascular interactions under COPD relevant oxidative stress

Haensel, M.; Millns, R.; Whitwell, H.; Ainscough, A. J.; van Batenburg-Sherwood, J.; Breuil, L.; Kostyunina, D.; Lloyd, C. M.; Wojciak-Stothard, B.

2026-06-09 bioengineering 10.64898/2026.06.04.730087 medRxiv
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Oxidative stress-induced airway injury contributes to chronic obstructive pulmonary disease (COPD). Cardiovascular complications increase COPD morbidity and mortality, but mechanistic links between airway injury and vascular dysfunction remain unclear, largely due to limitations of in vitro models that fail to replicate the multicellular lung environment. We developed REVAS, a modular organ-on-chip platform to study human respiratory-vascular cell-cell interactions at baseline and under oxidative stress conditions. REVAS consists of two respiratory chips hosting airway epithelium and microvascular endothelium, and a vascular chip hosting pulmonary artery endothelial cells co-cultured with vascular support cells, including smooth muscle cells, pericytes and fibroblasts. We studied effects of vascular support and respiratory cells on vascular endothelial phenotype at baseline and under H2O2-induced epithelial oxidative stress using functional assays, proteomic and transcriptomic analyses. Multicellular environment enhanced vascular endothelial barrier function and promoted respiratory and vascular cell differentiation at baseline. Mural cells altered endothelial cell-matrix interactions, metabolism and cytoskeletal remodelling, while respiratory cells promoted endothelial aerobic respiration and quiescent phenotype. Epithelial oxidative stress triggered inflammatory gene expression across all respiratory and vascular cells alongside apoptotic, reparative and pro-angiogenic signalling in endothelial and mural cells, accompanied by increased release of COPD-relevant cytokines and chemokines, including IL-6, TNF-/{beta}, IL-8, CCL5, CXCL9, PDGF, TGF-{beta}. Comparative analyses with COPD endothelial datasets confirmed that REVAS recapitulates key features of disease-associated endothelial dysfunction. These findings demonstrate that airway epithelial injury drives downstream vascular responses linked to inflammation and vascular remodelling, establishing REVAS as a human-relevant platform for mechanistic and therapeutic evaluation of cell-cell interactions in COPD and related lung diseases. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=164 HEIGHT=200 SRC="FIGDIR/small/730087v1_ufig1.gif" ALT="Figure 1"> View larger version (59K): org.highwire.dtl.DTLVardef@e29fd8org.highwire.dtl.DTLVardef@6c3d22org.highwire.dtl.DTLVardef@21a53forg.highwire.dtl.DTLVardef@e7f432_HPS_FORMAT_FIGEXP M_FIG C_FIG REVAS: a microfluidic platform developed to model multicellular interactions between airway epithelium and pulmonary vasculature under basal and oxidative stress. COPD: Chronic Obstructive Pulmonary Disease; EMT: endothelial-to-mesenchymal transition; HsEpCs: human small airway epithelial cells; HPMVECs: human pulmonary microvascular endothelial cells; HPAECs: human pulmonary artery endothelial cells; HPASMCs: human pulmonary artery smooth mucle cells; HPFs: human pulmonary fibcroblasts; HPCs: human pericytes.

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Hydrodynamic shear enables enrichment of functional tumor antigen-reactive T cells

Subramanian, P. S.; Fu, M.; Semaan, L. C.; Sher, A. S.; Shergill, B. S.; George, S. C.; Shirure, V. S.

2026-07-08 bioengineering 10.64898/2026.07.08.737133 medRxiv
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Adoptive T-cell therapies rely on the identification and expansion of rare tumor-reactive T cells, yet current enrichment strategies are limited by the low abundance of these cells and complexity of their functional enrichment. Here, we present a microfluidic platform that exploits hydrodynamic shear as a controllable parameter for enriching antigen-specific T cells through peptide-major histocompatibility complex (pMHC)-mediated capture. An eight-channel microfluidic device was engineered to simultaneously interrogate a range of wall shear stresses while maintaining uniform cell delivery, enabling systematic identification of shear conditions that maximize antigen-specific enrichment. Using engineered MART-1-specific Jurkat cells, we demonstrate that T-cell capture is jointly regulated by wall shear stress and pMHC density, with intermediate shear preferentially enriching antigen-specific cells over nonspecific binders. Translation of the optimal operating condition to a high-throughput single-shear device enabled approximately 35-fold enrichment of antigen-specific T cells from peripheral blood mononuclear cells containing only 0.05% target cells. We further show that peptide-MHC complexes isolated directly from melanoma whole-cell lysates support shear-dependent enrichment comparable to recombinant pMHCs. Finally, primary MART-1-specific CD8 T cells enriched using tumor-derived pMHCs retained the ability to recognize melanoma cells and upregulated the activation marker CD137 following antigen-specific stimulation. Together, these findings establish hydrodynamic shear as an orthogonal parameter for antigen-specific T-cell enrichment and provide a framework for integrating force-based selection with tumor-derived pMHCs to isolate functional antigen-specific T cells using tumor-derived pMHCs.

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Physics-Informed Operator Learning for Pulsatile Milk Flow in Distal Generations of a Bifurcated Mammary Duct Network

Olapojoye, A. O.; Nosratinia, A.; Hassanipour, F.

2026-06-16 bioengineering 10.64898/2026.06.12.731941 medRxiv
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Pulsatile milk transport through the lactating mammary ductal tree involves complex interactions between pressure gradients, wall compliance, and non-Newtonian rheology across spatial scales that span nearly two orders of magnitude in lumen radius. Direct experimental characterisation of flow in distal ductal generations remains infeasible due to their sub-millimetre calibre, leaving the haemodynamic environment of the secretory ductules largely unknown. We present a two-stage physicsinformed operator-learning framework that extends validated flow predictions from three instrumented duct generations to twenty generations of a bifurcated mammary network. A Physics-Informed Neural Network (PINN) trained against particle image velocimetry measurements across seven ducts achieved R2 = 0.924-0.997. A Deep Operator Network (DeepONet) distilled from the PINN and refined through physics-constrained training on the governing one-dimensional fluid-structure interaction equations achieved R2(u) = 0.857-0.985 across all validated ducts, with predictions for Generations 4-20 obtained by supplying Murrays Law geometry and mass-conservation-scaled boundary conditions to the frozen operator. Three biophysically significant findings emerge: a mean velocity plateau of 0.14-0.18 m/s across Generations 4-13 produced by Cross shear-thinning compensation offsetting Murray-branching deceleration; a non-monotonic pulsatility index that declines from 0.048 at Generation 1 to a minimum of 0.039 at Generation 5 before rising monotonically to 1.37 at Generation 20 as progressive wall stiffening drives the most distal ductules into a microcirculation-like haemodynamic regime; and a brief elastic-recoil transition zone at Generations 4-5 where mean axial pressure drop reverses sign. To the authors knowledge, these results provide the first quantitative characterisation of pulsatile milk flow across the full hierarchy of a bifurcated mammary ductal tree using a physics-informed operator-learning framework with implications for ductal mechanobiology, milk ejection mechanics, and mastitis pathogenesis.

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Cellfoundry: a GPU-accelerated, multi-physics ABM framework for cellular microenvironment and organoid-scale studies

Borau, C.; Chisholm, R.; Richmond, P.

2026-04-25 bioengineering 10.64898/2026.04.22.720218 medRxiv
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Advanced in vitro systems such as organoids and microfluidic organ-on-a-chip platforms enable physiologically richer experimentation, but their complexity creates large parameter spaces and makes it difficult to disentangle the mechanistic roles of transport, mechanics, and extracellular microstructure. Agent-based modelling provides a natural computational counterpart to these systems by representing heterogeneous cells as discrete entities coupled through local rules and environmental fields. However, realistic microenvironment models often remain limited by scalability, simplified extracellular matrix representations, and the practical difficulty of calibrating large numbers of parameters. Here we present Cellfoundry, a computational framework built on a FLAMEGPU2-based modelling template for simulating complex cellular microenvironments. The framework integrates multiple interacting agent populations, including cells, fibrous networks, and focal adhesions mediating attachment dynamics and traction-force transmission. It combines mechanically resolved cell-cell and cell-matrix interactions with multi-species diffusion fields that propagate biochemical signals through the extracellular environment and regulate processes such as metabolism, migration, and cell-cycle progression. Cellfoundry also supports customizable behaviours across multiple cell types, enabling the study of heterogeneous multicellular systems within a unified computational setting. To support reproducible model development and calibration, the framework includes a fibre-network generation module, automated performance benchmarking workflows, post-processing and reporting utilities, and an Optuna-based Bayesian optimization pipeline with configurable single- and multi-objective targets. Two showcase examples illustrate these capabilities: a migration assay calibrated against fibroblast motility descriptors and a multi-objective organoid growth scenario reproducing target population composition and expansion dynamics and over time. Together, these examples demonstrate how Cellfoundry can be used to build, calibrate, and extend mechanistically interpretable models of coupled biochemical and mechanical dynamics in advanced in vitro systems. HighlightsO_LIHighly versatile, GPU-accelerated agent-based framework for cellular microenvironments C_LIO_LIExplicit fibrous ECM networks with dynamic remodelling and focal adhesion agents C_LIO_LICoupled mechanics and multi-species diffusion regulate cell behaviour in a highly customizable environment C_LIO_LIModular architecture with automated benchmarking and Bayesian parameter optimization C_LI

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A High-Fidelity 3D Fluid-Structure Interaction Framework for Predictive Microfluidic Design

Shen, L.; Zhang, Y.; Chen, Y.; Ding, X.; Wen, P.; Wang, C.; Sun, P.; Gong, S.; Xu, J.; Han, J.; Chen, Y.

2026-04-30 bioengineering 10.64898/2026.04.28.721227 medRxiv
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The commercial maturation of microfluidics remains bottlenecked by empirical prototyping and an absence of predictive digital design capabilities. Because optimizing advanced technologies such as passive particle separation fundamentally hinges on the precise coupling of fluid dynamics and particle mechanics, conventional two-dimensional or decoupled fluid simulations inherently fail to capture authentic multiscale behaviors. To bridge this gap, we establish a high-fidelity three-dimensional fluid-structure interaction framework combining a high-order Arbitrary Lagrangian-Eulerian mapping-based finite element method with a localized hierarchical dynamic mesh strategy. Engineered to accurately resolve complex multiscale hydrodynamics, this architecture utilizes deterministic lateral displacement structures as a stringent test case. Validated against experimental data for rigid microspheres and tumor cells, the framework predicts transport trajectories and critical separation diameters with sub-micron precision. Crucially, the simulation explicitly resolves the M-shaped spatial fluctuation of local size thresholds alongside the dynamic vertical migration of particles. Unveiling these hidden physical mechanisms provides a deterministic explanation for highly debated phenomena such as mixed-mode transport. By enabling the rigorous in silico evaluation of complex non-periodic architectures, this framework serves as a powerful instrument for predictive structural optimization. Such capabilities establish the essential infrastructure for microfluidic digital design, accelerating the transition from empirical trial-and-error to precision simulation-driven engineering.

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A vascular chip for disease-relevant flow shear stress topology

Li, K.; Yang, S.; Hu, K.; Liang, Z.; Zhang, X.; Yang, J.; Morbiducci, U.; Mazzi, V.; Gallo, D.; Wang, L.; Wang, M.; Sun, X.; Chen, Z.; Sun, A.; Chang, L.; Chen, Y.; Zheng, Y.; Liu, X.

2026-07-07 bioengineering 10.64898/2026.07.07.736911 medRxiv
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Vascular chips have advanced endothelial mechanobiology by enabling controlled responses to hemodynamic cues, yet disease-relevant wall shear stress (WSS) modeling remains limited. Simplified one-dimensional flow shear systems, designed mainly for physiological mechanobiology, miss the topological organization of pathological flow, whereas patient-specific vascular models capture complex hemodynamics but sacrifice generality and imaging compatibility. Here we develop a programmable vascular chip that converts disease-associated WSS topology into a physiologically parameterized experimental input. The device reconstructs a representative pathological shear-topology field on endothelial layer, supports stationary and physiologically paced oscillatory flow modes, and integrates matched unidirectional-shear references within the same chip. Using this system, we show that oscillatory WSS topology destabilizes endothelial monolayers, drives asymmetric collective emergent behaviors, impairs actin-nuclear mechanotransduction, accompanied by nuclear softening and enhanced perinuclear nanoparticle uptake. Integrated live-cell imaging, fluorescence analysis, Brillouin microscopy, and transport assays enable multimodal phenotyping across collective, subcellular mechanical and functional scales. By making disease-relevant WSS topology experimentally controllable, this vascular-chip framework bridges computational hemodynamics and experimental mechanomedicine, supporting standardized vascular disease modeling and functional screening.

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A Cone-Plate Bioreactor for Applying Physiologically Derived Shear Stress Waveforms to Study Endothelial Mechanotransduction and Cardiac Cell Signaling

Watson, M. C.; Kemmerling, E. C.; Black, L. D.

2026-06-03 bioengineering 10.64898/2026.05.31.729120 medRxiv
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Fluid shear stress is a critical regulator of endothelial cell function and cardiovascular development, yet in vitro platforms often lack the ability to reproduce physiologically relevant, time-dependent flow environments with quantitative precision. Here, we present the design and validation of a macro-scale cone-plate bioreactor engineered to deliver controlled steady and pulsatile shear stress waveforms to endothelial monolayers and engineered tissues. The system integrates a geometry optimized to minimize secondary flow effects, a feedback-controlled motor capable of reproducing complex waveforms, and a viscosity-informed control framework to account for shear-dependent fluid behavior. Using this platform, endothelial cells were exposed to steady and physiologically derived pulsatile shear stresses. Cells exhibited increased alignment and eccentricity under shear, confirming biologically relevant mechanical stimulation. While pulsatile shear did not significantly alter endothelial neuregulin-1 expression, exogenous administration studies revealed a nonlinear, dose-dependent increase in cardiomyocyte proliferation. Furthermore, co-culture experiments demonstrated that shear-conditioned endothelial cells promote cardiomyocyte proliferation, suggesting a mechanotransduction-mediated paracrine signaling mechanism. Together, these results establish a versatile and quantitatively controlled platform for studying cardiovascular mechanobiology. This device enables systematic investigation of shear-dependent cellular responses and provides a foundation for integrating co-culture systems and three-dimensional engineered tissues under physiologically relevant hemodynamic conditions.

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Engineered Matrices Reveal Sulfation-Mediated Stress Adaptation and Drug-Specific Modulation of Chemotherapeutic Response

Sarica, S.; Ozturk, E.

2026-05-26 bioengineering 10.64898/2026.05.21.726894 medRxiv
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Engineering biomimetic extracellular matrices that isolate specific biochemical cues is essential for understanding how matrix chemistry regulates tumor cell behavior and therapeutic response. Aberrant sulfation due to proteoglycan expression is a hallmark of lung tumor matrices, yet its functional impact is difficult to study using conventional materials where mechanical and biochemical variables are coupled. To address this, mechanically matched sulfated alginate hydrogels are engineered to mimic the elevated sulfated glycosaminoglycan (sGAG) content of malignant ECM, enabling sulfation to be examined as a single, tunable variable. Within this system, ECM sulfation is shown to enhance tumor cell proliferation, promote oxidative and mitochondrial stress tolerance, suppress apoptotic signaling and attenuate the efficacy of cisplatin, gemcitabine and paclitaxel. Sulfated matrices preserve mitochondrial membrane potential, limit ROS accumulation, shift apoptotic gene expression toward a survival-favoring profile, selectively upregulate ABCB1-mediated efflux and modulate drug response through the PI3K/Akt-ABCB1 signaling axis. Functional inhibition of PI3K and ABCB1 uncovers drug-specific dependencies while dual pathway targeting completely restores chemotherapeutic sensitivity. These findings identify ECM sulfation as a potent regulator of stress adaptation and therapeutic efficacy in lung adenocarcinoma and underscore the importance of biomimetic ECM design in controlling tumor cell fate and drug response.

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Modeling the metabolic heterogeneity of high-grade serous ovarian cancer solid tumors in 3D Microphysiological systems

Manan Mejias, P. M.; Boonpattrawong, N.; Berube, M.; Letts, E. K.; Reed-McBain, F.; Peraza Munuzuri, A. S.; Vazquez, Y. N.; Patankar, M.; Virumbrales-Munoz, M.

2026-07-09 cancer biology 10.64898/2026.06.30.735360 medRxiv
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High-grade serous carcinoma (HGSOC) is the deadliest subtype of ovarian cancer, characterized by high metastatic rates. HGSOC is typically diagnosed at late stages, and treatment options are limited, resulting in a 60% recurrence rate. HGSOC cells exhibit metabolic plasticity, dynamically shifting between glycolysis and oxidative phosphorylation (OXPHOS) to meet energy demands for tumor progression. To evaluate therapeutic strategies that target metabolic vulnerabilities, we developed a microphysiological system (MPS) that recapitulates the heterogenous cell states and bioenergetic distribution of HGSOC solid tumors. Our platform utilized HGSOC spheroids embedded in a collagen hydrogel that mimics the extracellular matrix to capture tumor progression in the ovary. We used atovaquone (ATO), an FDA-approved OXPHOS inhibitor, to prototype the capabilities of our platform to investigate metabolic plasticity in HGSOC. Treatment with ATO decreased viability and invasion of HGSOC spheroids. Crucially, ATO exhibited no cytotoxicity toward biomimetic blood vessels, preserving their integrity and permeability. Metabolic imaging revealed that ATO induces an oxidative state in the outer region of the spheroids. At the invasive front, ATO disrupted mitochondrial organization, forcing collective cell migration and eventually inducing breakdown of mitochondrial networks. Furthermore, ATO decreased YAP/TAZ pathway activity in the outer region of the spheroid, providing a potential mechanism for hindered cell invasion. Collectively, our data demonstrates that a low-potency OXPHOS inhibitor like ATO can effectively target metabolic plasticity to suppress HGSOC spheroid progression. Overall, this platform successfully recapitulated metabolic heterogeneity and provided a workflow for safely testing other drugs that target cancer metabolism.

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Endothelial adaptation to complex flow patterns in a novel in vitro model predicted by computational fluid dynamics

Spurgin, S. B.; Salimi, S.; Lee-Kim, V. S.; Pramanik, T.; Mettlen, M.; Sadat, H.; Cleaver, O.

2026-07-09 cell biology 10.64898/2026.06.27.734995 medRxiv
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The endothelial cells (ECs) that line blood vessels continuously sense and respond to the physical forces exerted by blood flow. In vivo, pulsatile arterial flow interacts with vessel curvature, branching and other anatomical features to generate complex local hemodynamic environments that dictate the magnitude, direction, pulsatility, and oscillatory nature of wall shear stress experienced by ECs. Currently, accessible and reproducible in vitro models of complex pulsatile flow that recapitulate in vivo vascular anatomy remain limited. Here, we combine a novel rotational-flow endothelial culture platform with detailed computational fluid dynamics (CFD) modeling to characterize four well geometries designed to generate distinct hemodynamic environments. CFD analyses demonstrate that these geometries intrinsically generate pulsatile flow and produce reproducible spatially distinct regions of wall shear stress magnitude, pulsatility, and oscillatory shear within a single culture well. Endothelial alignment mapping and functional assays reveal region-specific cellular responses to the predicted local flow conditions that closely corresponded to the predicted local hemodynamic environment, linking complex flow patterns to endothelial adaptation. The technical advancements of our modeling efforts should support a faster, cheaper, simpler, and--importantly--validated framework for future investigation into EC mechanobiology under complex flow conditions. HIGHLIGHTSO_LISimple engineered well geometries generate distinct hemodynamic microenvironments, mimicking in vivo vascular structures, using a conventional orbital shaker. C_LIO_LIComputational fluid dynamics (CFD) reveals spatially distinct patterns of wall shear stress, pulsatility, and oscillatory shear applied to ECs within individual culture wells. C_LIO_LIHigh average wall shear stress and elevated oscillatory shear index induces a unique perpendicular alignment of ECs to the dominant flow vector. C_LI

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A Head and Neck Cancer Patient-Specific Microphysiological System for Predicting Response to Chemoradiation

Ahmed, A.; Hendrikse, N.; Schwartz, R. W.; Li, Y.; Lares, M.; Felix, C. K.; Burr, A. R.; Ong, I. M.; Harari, P. M.; Beebe, D. J.; Kerr, S. C.

2026-04-30 bioengineering 10.64898/2026.04.28.721391 medRxiv
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Head and neck cancer (HNC) is the 6th most common malignancy worldwide. 60% of patients present with advanced disease and approximately 50% of patients recur following primary treatment. Chemoradiation remains a standard of care for most patients. However, clinicians lack functional tools to predict which patients will respond to chemoradiation prior to treatment and current models, including organoids and animal model systems, fail to capture either full complexity or patient-to-patient heterogeneity of the individual HNC tumor and microenvironment (TME). Here, we have developed, characterized, and tested a patient-specific microphysiological system (MPS) that reconstructs the HNC TME in a vascularized 3D environment. This MPS was constructed from malignant cells, fibroblasts, and immune cells from a patients surgically resected tumor, seeded within a 3D hydrogel with molded endothelial lumens. Single-cell RNA sequencing confirmed that the MPS preserved 12 transcriptionally distinct cell populations found in matched native tissue. The platform recapitulated tumor hypoxia, with a 12-fold increase in hypoxic marker expression that altered radiation response, consistent with clinical HNC biology. Compartment-resolved imaging revealed distinct treatment dynamics in tumor, stromal, and vascular regions, and individual patients exhibited divergent responses to chemoradiation in spheroid morphology, cell viability, and migration. We found the slope of spheroid area change with treatment tracked with tumor recurrence, suggesting this metric could serve as a functional predictor of therapeutic response.

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Endothelial Heterogeneity Across Vascular Beds Impacts Inflammatory Signaling and Neutrophil Adhesion

Ginter, E. L.; Mitra, S.; Hind, L. E.

2026-05-29 bioengineering 10.64898/2026.05.26.727909 medRxiv
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Endothelial cells (ECs) are key players in maintaining homeostasis and coordinating immune responses, activating during acute inflammation to recruit immune cells. Endothelial heterogeneity has been found to impact transcription level differences across EC sources, but how these differences drive downstream effects in inflammatory signaling and immune interactions remains unclear. Here, we employed multiplexed ELISA to quantify secretion for 19 inflammatory factors following tumor necrosis factor (TNF) or Pseudomonas aeruginosa activation of four primary human EC sources: umbilical artery (HUAEC), umbilical vein (HUVEC), dermal microvascular (HDMEC), and pulmonary microvascular (HPMEC) endothelial cells. We also quantified changes in neutrophil adhesion to each EC source and used partial least squares regression (PLSR) to identify key inflammatory proteins associated with changes in neutrophil adhesion. We found distinct inflammatory secretion profiles across all cell types, with veinous ECs showing the highest basal secretion of most inflammatory proteins and pulmonary ECs exhibiting the lowest. Arterial ECs exhibited the lowest sensitivity to inflammatory stimulus, while pulmonary ECs exhibited dynamic responses following activation. Furthermore, inflammatory stimulus caused large differences in expression across cell sources for six factors: GM-CSF, IL-1{beta}, IL-6, IP-10, E-selectin, and ICAM-1. We found endothelial heterogeneity also contributed to differences in neutrophil adhesion to unstimulated ECs. Our PLSR analysis revealed five secreted factors most indicative of changes in neutrophil adhesion: E-selectin, ICAM-1, PECAM1, IL-6, and IL-8. Collectively, our findings strengthen the emerging view that vascular-bed specific differences in EC phenotype can impact downstream immune responses.

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Fluid shear stress modulates endocytic pathways and junctional targeting of tumor-derived extracellular vesicles in endothelial cells

Jones Villarinho, N.; Sung, B. H.; Yamagata, A. S.; Gomes Teles, R. H.; Da Silva, L.; Zelanis, A.; Salardani, M.; Costa Cruz, M.; Ramos Tercaroli, G.; Samartin, V.; Bernardi, J.; Gastaldoni Jaeger, R.; Weaver, A.; Freitas, V.

2026-05-05 cancer biology 10.64898/2026.05.01.721946 medRxiv
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Breast cancer is the most common malignancy in women, with triple-negative breast cancer (TNBC) representing the most aggressive subtype and carrying a poor metastatic prognosis. Metastasis requires tumor cells to cross the endothelial barrier, a process facilitated by tumor-derived extracellular vesicles (EVs), which can disrupt vascular integrity. Fluid shear stress (FSS), generated by blood flow, shapes endothelial physiology and may influence EV uptake, yet the mechanisms underlying TNBC-derived small EV (sEV) internalization remain unclear. Here, we investigated TNBC sEV-endothelial interactions using combined in silico and in vitro approaches. Human umbilical vein endothelial cells (HUVECs) were cultured under static or FSS conditions (20 dyn/cm{superscript 2}), followed by proteomic profiling and protein-protein interaction analyses with sEV proteomes. Uptake assays employed pharmacological inhibition (Dynasore, M{beta}CD, Pitstop2), Caveolin-1 (CAV-1) and Clathrin Heavy Chain (CLHC), siRNA-mediated knockdown, and junctional interaction analyses via confocal microscopy and co-immunoprecipitation. FSS downregulated proliferation- and angiogenesis-associated proteins while upregulating adhesion and cytoskeletal regulators assessed by proteomics. Network analysis identified clathrin- and caveolin-mediated endocytosis (CME and CavME), integrins, and early endosomes as central mediators of sEV uptake. Functionally, uptake was reduced by Pitstop2, M{beta}CD, and CAV-1/CLHC knockdown under static conditions, but silencing paradoxically enhanced uptake under FSS, suggesting compensatory flow-dependent pathways. Notably, under FSS, sEVs accumulated at endothelial junctions, colocalizing with VE-CAD and associating with CLDN5, indicating a potential disruption mechanism of adherens and tight junctions and consequent endothelial permeability. These findings identify CME and CavME as key uptake routes while underscoring FSS as a critical determinant of endothelial-tumor EV interactions. By revealing junctional targeting of sEVs, this work provides new mechanistic insight into vascular remodeling during metastasis and highlights EV pathways as potential therapeutic targets in TNBC. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/721946v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@f91c5org.highwire.dtl.DTLVardef@2b4dc8org.highwire.dtl.DTLVardef@ff94f1org.highwire.dtl.DTLVardef@18b714b_HPS_FORMAT_FIGEXP M_FIG C_FIG Uptake and localization of sEVs on HUVEC under (a) static and (b) fluid shear-stress conditions. sEVs: Small Extracellular Vesicles. CME: Clathrin-mediated Endocytosis. CavME: Caveolin-mediated Endocytosis. CLDN5: Claudin-5. VE-CAD: Vascular Endothelial Cadherin. FSS: Fluid shear-stress.

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Electroadhesion of polymer networks by polycation interfacial bridging: sticky electrophoresis, ionic complexation, and chain entanglement

Ying, B.; Yu, K.-H.; Yang, S.; Yang, J.

2026-06-10 bioengineering 10.64898/2026.06.05.730541 medRxiv
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An e-GLUE is a polymer network containing interpenetrating polycations, which can bond the anionic network of mucosa through interfacial polycation bridging under an electric field. Such an electroadhesion involves electrophoresis of polycations, ionic complexation between polycations and the anionic network, and polycation-network entanglement, yet their quantitative understanding is lacking. Here, we formulate a theoretical model to describe electroadhesion of polymer networks by polycation interfacial bridging. We use a diffusion-drift model coupled with a Bell-like field-dependent chain friction to describe the sticky electrophoresis of polycations in an anionic sea. The formation of ionic bonds is determined by local availability of cations and anions over the penetration depth. To debond, a force must either pull polycations out from the e-GLUE network or first dissociate them from ionic complexes and then pull out from the anionic network. We model chain pullout from the bulk networks to the interface as a viscous drag against water. The adhesion strength is calculated by summing the debonding force for each polycation per unit area across all chains. Our model quantitatively links electric field strength, applied duration, polycation chain length, and cation concentration to polycation electrophoresis kinetics, ionic bond formation, and adhesion strength. We further conduct electroadhesion tests, and our model predicts well with the experimental data. Lastly, we discuss the use of the model to guide the e-GLUE design. TOC graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/730541v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@16524c6org.highwire.dtl.DTLVardef@15163aeorg.highwire.dtl.DTLVardef@673949org.highwire.dtl.DTLVardef@e207a0_HPS_FORMAT_FIGEXP M_FIG C_FIG For Table of Contents use only

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Identifying cytokine-release signatures of flow-driven endothelial remodelling in an intracranial aneurysm cell culture model

De Nys, C. M.; Sardenberg Lima, T. G.; Anbananthan, H.; Mitchell, T.; Mansi, S.; Binder, A.; Li, Z.; Novak, J. I.; Mela, P.; Wise, S. G.; Carluccio, D.; Winter, C. D.; Murphy, A. R.; Franco, R. A.; Allenby, M. C.

2026-06-20 bioengineering 10.64898/2026.06.18.733289 medRxiv
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Intracranial aneurysm (IA) rupture is catastrophic, yet current models of rupture-risk inadequately capture underlying IA remodelling mechanisms. Endothelial-haemodynamic interactions are central to these processes, but in vitro flow platforms often lack vessel-relevant geometry or long-term perfusion. Here, temporal and spatial endothelial responses to haemodynamic stress were investigated across idealised and patient-specific vascular models. Polydimethylsiloxane models were endothelialised with human aortic endothelial cells then perfused at up to 1.6 Pa wall shear stress for five days. IA models were exposed to steady or cardiovascular flow waveforms, with endothelial phenotype assessed by immunofluorescence and cytokine profiling. Flow initiation induced a transient inflammatory response, with elevated MCP-1 and TNF- at day two, followed by a resolution of cytokine levels by day five, including a [~]7.5-fold reduction in MCP-1, despite increased haemodynamic loading. Endothelial cells retained a cobblestone-like morphology with eNOS undetected, resembling a partially activated phenotype. Compared with steady flow, cardiovascular flow reduced TGF-{beta}1 and IL-8 secretion and decreased FGF-b consumption ([~]2.5 fold), suggesting enhanced phenotypic stability. This study presents the first in vitro IA model incorporating a cardiovascular flow waveform and identifies cytokine signatures with potential utility as biomarkers of IA remodelling, highlighting the importance of long-term perfusion for modelling chronic vascular disease. Table of Contents FigureAn in vitro model of an intracranial aneurysm was developed to investigate how fluid flow dynamics impact endothelial remodelling and inflammation. Pulsatile cardiac flow promoted stabilisation of inflammatory signalling, which was sustained under a steady flow regime. Cytokine signatures emerged with potential utility as biomarkers of IA remodelling, highlighting the importance of long-term perfusion for modelling chronic vascular disease. The schematic of the cytokine release dynamics used in the graphical abstract below was generated with the assistance of AI-based tools including ChatGPT (v5.5) and M365 Copilot to align with key results from this manuscript. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=182 SRC="FIGDIR/small/733289v1_ufig1.gif" ALT="Figure 1000"> View larger version (80K): org.highwire.dtl.DTLVardef@c00d12org.highwire.dtl.DTLVardef@9a3afaorg.highwire.dtl.DTLVardef@1961b66org.highwire.dtl.DTLVardef@1e0fec5_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Cyclic stretch inhibits cell invasion in 3D scaffolds

Mungai, R. W.; Li, J.; Baines, J. L.; Kahugu, L. W.; Billiar, K. L.

2026-06-17 bioengineering 10.64898/2026.06.13.732094 medRxiv
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BackgroundThe development of clinically viable tissue-engineered heart valves (TEHVs) remains limited by inconsistent host cell infiltration. The dynamic hemodynamic environment may play a central role in driving or inhibiting cell invasion, yet the effects of cyclic stretch on cell migration and proliferation remain largely unexplored in 3D tissues and scaffolds. Given evidence that uniaxial constraint promotes directional invasion in 3D matrices, we hypothesized that uniaxial cyclic stretch would enhance cell invasion, particularly along the stretch direction. MethodsWe embedded multicellular spheroids into collagen hydrogels and subjected them to uniaxial cyclic stretch (3-10%, 1 Hz) for two days and quantified invasion into the surrounding extracellular matrix using a custom image-processing program. Smooth muscle cells, valvular interstitial cells, and dermal fibroblasts were examined to represent cell populations relevant to TEHVs and for comparison across cell types with different contractility. To determine the mechanisms underlying changes in invasion with stretch, effects of cell tension were evaluated using gel compaction assays and inhibition of myosin IIA, and proliferation was assessed by Ki67 immunostaining. ResultsContrary to our hypothesis, cyclic stretch profoundly inhibited cell invasion into the matrix across all cell types and magnitudes of stretch. Invasion decreased by >50% in smooth muscle cells and fibroblasts and by up to 99% in valvular interstitial cells. Invasion suppression was inversely correlated with cell contractility, implicating a role for cell-generated tension. Inhibition of myosin IIA partially rescued invasion with stretch, though not to static levels. Stretched spheroids also exhibited reduced cell proliferation relative to static controls. ConclusionsThese findings implicate actomyosin-mediated mechanotransduction in stretch-induced suppression of cell invasion and suggest that the dynamic valve environment may limit host-cell repopulation of TEHVs. More broadly, this work provides insight into how cyclic stretch regulates 3D cell invasion in mechanically active tissues with implications for wound healing and cancer metastasis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=167 SRC="FIGDIR/small/732094v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@2a21b1org.highwire.dtl.DTLVardef@9fbf6org.highwire.dtl.DTLVardef@17ceb17org.highwire.dtl.DTLVardef@2e3bf9_HPS_FORMAT_FIGEXP M_FIG C_FIG