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APL Bioengineering

AIP Publishing

All preprints, 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. Older preprints may already have been published elsewhere.

1
Coupling of perinuclear actin cap and nuclear mechanics regulates flow-induced YAP spatiotemporal nucleocytoplasmic transport

Ma, T.; Liu, X.; Su, H.; Li, S.; Gao, C.; Liang, Z.; Zhang, D.; Zhang, X.; Li, K.; Hu, K.; Wang, L.; Wang, M.; Wu, F.; Yue, S.; Hong, W.; Chen, X.; Deng, X.; Wang, P.; Fan, Y.

2022-11-17 bioengineering 10.1101/2022.11.15.516697 medRxiv
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Mechanical forces, including flow shear stress, regulate fundamental cellular process by modulating the nucleocytoplasmic transport of transcription factors, such as Yes-associated Protein (YAP). However, the mechanical mechanism how flow induces the nucleocytoplasmic transport remains largely unclear. Here we found that unidirectional flow applied to endothelial cells induces biphasic YAP nucleocytoplasmic transport with initial nuclear import, followed by nuclear export as perinuclear actin cap forms and nuclear stiffening in a dose and timing-dependent manner. In contrast, pathological oscillatory flow induces slight actin cap formation and nuclear softening, sustaining YAP nuclear localization. To explain the disparately spatiotemporal distribution of YAP, we developed a three-dimensional mechanochemical model considering coupling processes of flow sensing, cytoskeleton organization, nucleus mechanotransduction, and YAP spatiotemporal transport. We discovered that actin cap formation and nuclear stiffness alteration under flow synergically regulate nuclear deformation, hence governing YAP transport. Furthermore, we expanded our single cell model to a collective vertex framework and found that actin cap irregularities in individual cells under flow shear stress potentially induce topological defects and spatially heterogeneous YAP distribution in cellular monolayers. Our work unveils the unified mechanism of flow-induced nucleocytoplasmic transport, offering a universal linkage between transcriptional regulation and mechanical stimulation.

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IntravChip: a vascularized and perfused microfluidic model of the primary tumor microenvironment to collect intravasated tumor cells

Floryan, M.; Cordiale, A.; Jensen, H.; Chen, J.; Guo, Z.; Vinayak, V.; Kheiri, S.; Raman, R.; Shenoy, V.; Cambria, E.; Kamm, R.

2026-02-20 bioengineering 10.64898/2026.02.19.706805 medRxiv
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Hematogenous metastasis is initiated when tumor cells (TCs) intravasate into the vasculature, yet intravasation remains poorly understood because it is difficult to observe in vivo and intravasated TCs are challenging to isolate. To address these challenges, we developed IntravChip, a continuously perfused microfluidic platform containing a vascularized primary tumor microenvironment (TME) enabling the observation of TC intravasation, and a downstream chamber to collect intravasated TCs. The IntravChip can support a high TC concentration in the TME while maintaining complete vascular perfusion, which we found was necessary to collect intravasated cells. Using MDA-MB-231 breast TCs, we identified an optimal initial TC seeding density that, by day 9, yields a densely populated TME and 100-440 collected intravasated TCs. We validated the IntravChip across several TC types, showing that MDA-MB-231 and MV3 TCs have the highest intravasation rates while MCF-7 TCs have low intravasation efficiency. We also show that the IntravChip is compatible with super-resolution nano-imaging. Our devices enabled high-quality STORM imaging, which revealed that H3K9me3 nanodomains are significantly differentially distributed in intravasated MDA-MB-231 tumor cells compared to those residing in the TME. Finally, the IntravChip was validated as a platform to test the effects of anti-cancer drugs on tumor cells and on the vasculature. We showed that a 5 M concentration of sorafenib reduced intravasation events by 69% without impacting the morphology of the microvascular networks (MVNs), while a 10 M concentration led to a significant decrease in vessel diameter. This platform enables quantitative analysis of TC intravasation, collection of intravasated TCs for characterization, and screening of anti-metastatic therapies.

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Optical Cellular Micromotion: A New Paradigm to Measure Tumour Cells Invasion in 3D Tumour Environments

Guo, Z.; Yang, C.-T.; Chien, C.-C.; Selth, L.; Bagnaninchi, P.; Thierry, B.

2021-08-27 bioengineering 10.1101/2021.08.26.457857 medRxiv
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Measuring tumour cell invasiveness through three-dimensional (3D) tissues, particularly at the single cell level, can provide important mechanistic understanding and assist in identifying therapeutic targets of tumour invasion. However, current experimental approaches, including standard in vitro invasion assays, have limited physiological relevance and offer insufficient insight about the vast heterogeneity in tumour cell migration through tissues. To address these issues, here we report on the concept of optical cellular micromotion, where digital holographic microscopy (DHM) is used to map the optical thickness fluctuations at sub-micron scale within single cells. These fluctuations are driven by the dynamic movement of subcellular structures including the cytoskeleton and inherently associated with the biological processes involved in cell invasion within tissues. We experimentally demonstrate that the optical cellular micromotion correlates with tumour cells motility and invasiveness both at the population and single cell levels. In addition, the optical cellular micromotion significantly reduced upon treatment with migrastatic drugs that inhibit tumour cell invasion. These results demonstrate that micromotion measurements can rapidly and non-invasively determine the invasive behaviour of single tumour cells within tissues, yielding a new and powerful tool to assess the efficacy of approaches targeting tumour cell invasiveness. Significance StatementTumour cells invasion through tissues is a key hallmark of malignant tumour progression and its measurement is essential to unraveling biological processes and screening for new approaches targeting cell motility. To address the limitations of current approaches, we demonstrate that sub-micron scale mapping of the dynamic optical thickness fluctuations within single cells, referred to as optical cellular micromotion, correlates with their motility in ECM mimicking gel, both at the population and single cell levels. We anticipate that 3D optical micromotion measurement will provide a powerful new tool to address important biological questions and screen for new approaches targeting tumour cell invasiveness.

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Personalized models of breast cancer desmoplasia reveal biomechanical determinants of drug penetration

Offeddu, G. S.; Haase, K.; Wan, Z.; Possenti, L.; Nguyen, H. T.; Gillrie, M. R.; Hickman, D.; Knutson, C. G.; Kamm, R. D.

2021-12-13 bioengineering 10.1101/2021.12.12.472296 medRxiv
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Breast cancer desmoplasia heterogeneity contributes to high disease mortality due to discrepancies in treatment efficacy between patients. Personalized in vitro breast cancer models can be used for high throughput testing and ranking of therapeutic strategies to normalize the aberrant microenvironment in a patient-specific manner. Here, tumoroids assembled from patient-derived cells cultured in microphysiological systems including perfusable microvasculature reproduce key aspects of stromal and vascular dysfunction. Increased hyaluronic acid and collagen deposition, loss of vascular glycocalyx and reduced perfusion, and elevated interstitial fluid pressure in the models result in impaired drug distribution to tumor cells. We demonstrate the application of these personalized models as tools to rank molecular therapies for the normalization of the tumoroid microenvironment and to discover new therapeutic targets such as IL8 and CD44, which may ultimately improve drug efficacy in breast cancer patients.

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Sp1 mechanotransduction regulates breast cancer cell invasion in response to multiple tumor-mimicking extracellular matrix cues

Sharma, A.; Steger, R. F.; Li, J. M.; Baude, J. A.; Heom, K. A.; Dey, S. S.; Stowers, R. S.

2025-03-19 bioengineering 10.1101/2025.03.18.643983 medRxiv
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Breast cancer progression is marked by extracellular matrix (ECM) remodeling, including increased stiffness, faster stress relaxation, and elevated collagen levels. In vitro experiments have revealed a role for each of these factors to individually promote malignant behavior, but their combined effects remain unclear. To address this, we developed alginate-collagen hydrogels with independently tunable stiffness, stress relaxation, and collagen density. We show that these combined tumor-mimicking ECM cues reinforced invasive morphologies and promoted spheroid invasion in breast cancer and mammary epithelial cells. High stiffness and low collagen density in slow-relaxing matrices led to the greatest cell migration speed and displacement. RNA-seq revealed Sp1 target gene enrichment in response to both individual and combined ECM cues, with a greater enrichment observed under multiple cues. Notably, high expression of Sp1 target genes upregulated by fast stress relaxation correlated with poor patient survival. Mechanistically, we found that phosphorylated-Sp1 (T453) was increasingly located in the nucleus in stiff and/or fast relaxing matrices, which was regulated by PI3K and ERK1/2 signaling, as well as actomyosin contractility. This study emphasizes how multiple ECM cues in complex microenvironments reinforce malignant traits and supports an emerging role for Sp1 as a mechanoresponsive transcription factor.

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Topological evolution of sprouting vascular networks: from day-by-day analysis to general growth rules.

Rojek, K. O.; Wrzos, A.; Zukowski, S.; Bogdan, M.; Lisicki, M.; Szymczak, P.; Guzowski, J.

2023-09-06 bioengineering 10.1101/2023.09.02.555959 medRxiv
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Engineering tissues with an embedded vasculature of well-controlled topology remains one of the basic problems in biofabrication. Still, little is known about the evolution of topological characteristics of vascular networks over time. Here, we perform a high-throughput day-by-day analysis of tens of microvasculatures that sprout from endothelial-cell coated micrometric beads embedded in an external fibrin gel. We use the bead-assays to systematically analyze (i) macroscopic observables such as the overall length and area of the sprouts, (ii) microscopic observables such as the lengths of segments or the branching angles and their distributions, as well as (iii) general measures of network complexity such as the average number of bifurcations per branch. We develop a custom angiogenic image analysis toolkit and track the evolution of the networks for at least 14 days of culture under various conditions, e.g., in the presence of fibroblasts or with added endothelial growth factor (VEGF). We find that the evolution always consists of three stages: (i) an inactive stage in which cells remain bound to the beads, (ii) a sprouting stage in which the sprouts rapidly elongate and bifurcate, and (iii) the maturation stage in which the growth slows down. We show that higher concentrations of VEGF lead to an earlier onset of sprouting and to a higher number of primary branches, yet without significantly affecting the speed of growth of the individual sprouts. We find that the mean branching angle is weakly dependent on VEGF and typically in the range of 60-75 degrees suggesting that, by comparison with the available Laplacian growth models, the sprouts tend to follow local VEGF gradients. Finally, we observe an exponential distribution of segment lengths, which we interpret as a signature of stochastic branching at a constant bifurcation rate (per unit branch length). Our results, due to high statistical relevance, may serve as a benchmark for predictive models and reveal how the external means of control, such as VEGF concentration, could be used to control the morphology of the vascular networks. We provide guidelines for the fabrication of optimized microvasculatures with potential applications in drug testing or regenerative medicine.

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A microfluidic rheometer for tumor mechanics and invasion studies

Suh, Y. J.; Liu, M.; Zhu, B.; Pandey, M.; Cheung, B. C. H.; Kim, J.; Bouklas, N.; Roh, C.; Segall, J. E.; Hui, C. Y.; Wu, M.

2025-10-01 bioengineering 10.1101/2025.09.29.679368 medRxiv
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Clinically, the feel, touch, and shape of a solid tumor are important diagnostic methods for determining the malignant state of the disease. However, there are limited tools for quantifying the mechanics and the malignancy of the tumor in a physiologically realistic setting. Here, we developed a microfluidic rheometer - termed the microrheometer - that enables simultaneous measurements of tumor spheroid mechanics and their invasiveness into a 3D extracellular matrix (ECM). The microrheometer consists of a pneumatic pressure control unit for applying controlled static or cyclic compression to tumor spheroids, and a sample chamber for containing spheroid embedded ECM. The innovation here lies in the integration of a polyacrylamide membrane force sensor within the sample chamber, enabling a direct force measurement in a physiologically relevant setting. We found that both tumor stiffness and the viscoelastic properties of the tumor are closely correlated with tumor invasiveness. The microrheometer allowed us to measure tumor mechanics in a short time (less than a minute) and has the potential to be used clinically in the future. We note that the microrheometer here can be easily extended to studies of mechanics of single cell, nucleus, as well as other cell/tissue types.

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A data-informed approach for engineering in-vitro experiment design to decipher key features of invasive breast cancer cell phenotypes

Shah, L. V.; Breschi, V.; Tirella, A.

2025-03-25 bioengineering 10.1101/2025.03.21.643499 medRxiv
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The intrinsic complexity of biological processes often hides the role of dynamic microenvironmental cues in the development of pathological states. The use of micro-physiological systems (MPS) offers new technological platforms designed to model the dynamics of tissue-specific microenvironments in vitro and to holistically understand healthy and pathological states. In our previous works, we reported on engineering breast critical tumor microenvironment features, including matrix stiffness, pH, and fluid flow, and use the MPSs to study breast cancer cells phenotypes. By studying different microenvironments mimicking normal and tumor breast tissues, we obtained high-dimensional data using two distinctive human breast cell lines (i.e., MDA-MB231, MCF-7) investigating biomarkers commonly used in cancer in vitro models as cell proliferation, epithelial-to-mesenchymal transition (EMT), and breast cancer stem cell markers (B-CSC). We herein report on a new approach used to explore the complexity of MPSs and the high dimensional datasets: we introduce an innovative machine learning (ML) based platform employing unsupervised k-means clustering and feature extraction to identify key markers that differentiated invasive from non-invasive breast cell phenotypes. This novel data-driven approach streamlines experimental design and emphasizes the translational potential of integrating MPS-derived insights with ML to refine prognostic tools and personalize therapeutic strategies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/643499v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@4f947eorg.highwire.dtl.DTLVardef@9e1aedorg.highwire.dtl.DTLVardef@1f9fe8corg.highwire.dtl.DTLVardef@1b6b91d_HPS_FORMAT_FIGEXP M_FIG C_FIG

9
VEGF-A/C co-stimulation, without shear stress, triggers the polarization of lymphatic microvessels

bancaud, a.; Edwards, J.; Alric, B.; Morfoisse, F.; Garmy-Susini, B.; matsunaga, y. t.

2025-08-18 bioengineering 10.1101/2025.08.13.670220 medRxiv
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The lymphatic system maintains interstitial fluid homeostasis and supports immune function through dynamic regulation of its architecture mediated by molecular signals--such as vascular endothelial growth factors (VEGFs)--and physical cues. While VEGFs are known to promote endothelial proliferation, their broader roles in tissue organization remain under investigation. Using a lymphatic vessel-on-a-chip platform, we examine how lymphatic endothelial cells (LECs) respond to VEGF-A, VEGF-C, or their combination. We find that co-stimulation synergistically enhances lymphangiogenic sprouting while preserving barrier integrity. Co-stimulation also induces axial polarization of the tissue along the vessel axis, even in the absence of external mechanical stimuli. This polarization requires activation of the VEGFR2/VEGFR3 heterodimer and is disrupted by inhibition of the Src-dependent mechanotransduction pathway. Further co-stimulation enhances LEC motility and triggers vessel contraction. Modeling suggests that the tubular geometry of the lymphatic monolayer imposes intrinsic mechanical anisotropy--softer in the circumferential than axial direction. This geometrically-encoded stiffness landscape directs cell migration along the stiffer axis, uncovering a form of durotaxis driven by curvature-induced anisotropy. These results highlight a previously unrecognized mechanism by which biochemical and biophysical cues direct lymphatic tissue polarization, offering new insight into how geometry and mechanosensing shape lymphatic function.

10
High-throughput Genome Wide CRISPR Knock Out mechanical sort identifies genes driving metastatic cancer cell softening

Young, K. M.; Dobrowolski, C. N.; Stone, N. E.; Paunovska, K.; Bules, S.; Ahkee, K.; Hankish, J.; Chapman, A.; Dahlman, J. E.; Sulchek, T. A.; Reinhart-King, C. A.

2026-02-12 bioengineering 10.64898/2026.02.12.705447 medRxiv
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Cell mechanics can serve as an important biomarker for cell state and phenotype, such as metastatic ability. While some molecular mechanisms underlying cell mechanical properties have been investigated through targeted analyses, a genome-wide study of human genes and gene networks that modulate cell biophysical properties has not been attempted. In this work, we combined a microfluidic stiffness-based sorting device with a genome-scale CRISPR knockout (GeCKO) screen in order to investigate the effect of individual gene knockouts on cell stiffening and cell softening across the entire protein-coding genome. We processed approximately 150 million Cas9-expressing ovarian cancer cells that had been transduced with a library of 76,000 single guide RNAs (sgRNAs) against the 19,000 protein-coding genes in the genome. The cells were sorted into 5 mechanical subsets. We identified 7 gene knockouts that were significantly depleted in the softer subsets and over 700 gene knockouts that were significantly enriched in the stiffer subsets. Of these significant genes of interest, we selected 3 genes that were highly expressed in our ovarian cancer cell line with greater than 100-fold enrichment in the stiff outlet and resulted in significant changes in ovarian cancer patient survival. These genes, PIK3R4, CCDC88A, and GSK3B, when knocked out result in a significant and predicted increase in cell stiffness. This study is the first to explore the relation between human gene expression and cell mechanics at the genome-scale to generate datasets at the intersection between cell genotype, mechanotype, and phenotype for metastatic cancer cells. The method could also be applied to study the effect of genes on other biophysical cell processes as well as for identifying pathways for the control of cellular mechanics across many cell types.

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Tuning mechanical milieux of tissue templates and their cellular inhabitants to guide mechanoadaptation

Putra, V. L.; Sansalone, V.; Kilian, K. A.; Tate, M. L. K.

2024-12-07 bioengineering 10.1101/2024.12.03.626678 medRxiv
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Mechanomics describes the adaptation of mesenchymal stem cells (MSCs) to their mechanical environment, via cytoskeletal remodeling, as well as changes in shape and volume, ultimately resulting in emergent lineage commitment. Here we elucidated effects of exogenous microtubule stabilization, using paclitaxel (PAX), on stem cells capacity to sense and adapt to changes in their local mechanical environment. We studied the interplay between the living, evolving cells and their mechanical environment using established experimental and computational tools for respective delivery and prediction of shape and volume changing stresses. Stiffened and volumetrically larger microtubule-stabilized MSCs and their experienced significantly different normal and shear stress compared to control cells when exposed to identical bulk laminar flow (0.2 dyn/cm2) for one hour. These spatiotemporal mechanical cues transduced to the nucleus via the cytoskeleton, triggering significantly different changes in gene expression indicative of emergent lineage commitment than those observed in control cells. Using a paired computational model, we further predicted a range of mechanoadaptation responses of microtubule-stabilized cells to scaled up flow magnitudes (1 and 2 dyn/cm2). Hence, MSCs adapt to as well as modulate their own mechanical environment via cytoskeletal remodeling and lineage commitment - microtubule stabilization changes not only MSCs mechanoadaptive machinery, their capacity to adapt, and their lineage commitment, but also their mechanical environment. Taken as a whole, these studies corroborate our working hypothesis that MSCs and their mechanoadaptive machinery serve as sensors and actuators, intrinsically linked to their lineage potential via mechanoadaptive feedback loops which are sensitive to exogenous modulation via biochemical and biophysical means. ClassificationBiological Systems Engineering, Computational Simulations, Cell Biology, Biophysics

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Three-Dimensional Bioconjugated Liquid-Like Solid (LLS) Enhance Characterization of Solid Tumor - Chimeric Antigen Receptor T cell Interactions

Nguyen, D. T.; Liu, R.; Ogando-Rivas, E.; Pepe, A.; Pedro, D.; Qdaisat, S.; Nguyen, T. Y. N.; Lavrador, J.; Golde, G.; Smolcheck, R.; Ligon, J.; Jin, L.; Tao, H.; Webber, A.; Phillpot, S.; Mitchell, D.; Sayour, E. J.; Huang, J.; Castillo, P.; Sawyer, W. G.

2023-02-21 bioengineering 10.1101/2023.02.17.529033 medRxiv
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Cancer immunotherapy offers lifesaving treatments for cancers, but the lack of reliable preclinical models that could enable the mechanistic studies of tumor-immune interactions hampers the identification of new therapeutic strategies. We hypothesized 3D confined microchannels, formed by interstitial space between bio-conjugated liquid-like solids (LLS), enable CAR T dynamic locomotion within an immunosuppressive TME to carry out anti-tumor function. Murine CD70-specific CAR T cells cocultured with the CD70-expressing glioblastoma and osteosarcoma demonstrated efficient trafficking, infiltration, and killing of cancer cells. The anti-tumor activity was clearly captured via longterm in situ imaging and supported by upregulation of cytokines and chemokines including IFNg, CXCL9, CXCL10, CCL2, CCL3, and CCL4. Interestingly, target cancer cells, upon an immune attack, initiated an "immune escape" response by frantically invading the surrounding microenvironment. This phenomenon however was not observed for the wild-type tumor samples which remained intact and produced no relevant cytokine response. Single cells collection and transcriptomic profiling of CAR T cells at regions of interest revealed feasibility of identifying differential gene expression amongst the immune subpopulations. Complimentary 3D in vitro platforms are necessary to uncover cancer immune biology mechanisms, as emphasized by the significant roles of the TME and its heterogeneity.

13
A scalable tumor-vasculature-on-chip for CAR T cell trafficking and efficacy studies

de Haan, L.; Olczyk, A.; Olivier, T.; Wesselius, J.; Suijker, J.; Al-Mardini, C.; Burton, T.; van den Broek, L.; Queiroz, K.

2026-02-09 bioengineering 10.64898/2026.02.05.703975 medRxiv
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Most cellular therapies, like CAR T cells, remain ineffective in solid tumors. This is primarily due to a complex tumor microenvironment (TME), which creates biochemically hostile and often immunosuppressive conditions that limit efficacy of immunotherapies. Besides, cellular therapy efficacy is still often established in traditional 2D cultures that fail to simulate relevant aspects of solid tumor biology. Recent advances in three-dimensional (3D) and organ-on-chip culture systems have provided more physiologically relevant models for immunotherapy testing. These microphysiological systems (MPS) not only offer a 3D environment that alters tumor cell sensitivity to therapy but also enable inclusion of TME components and assessment of processes such as extravasation and infiltration, key steps in CAR T cell activity in vivo. This study focuses on applying an advanced culture technique and further building on the use of a scalable on-chip platform, the OrganoPlate, to grow EpCAM-positive and EpCAM-negative tumor cells in co-culture with an endothelial vessel to study EpCAM-targeting CAR T cell migration and killing kinetics. The CAR T cells specifically targeted and killed EpCAM-positive HT-29 tumor cells while EpCAM-negative A375 tumor cells were not affected. In addition, target cell killing was dependent on the ratio between CAR T and tumor cells (E:T ratio) and was enhanced by addition of IL-2. Inflammatory cytokines like INF-{gamma}, TNF and IL-6 increased overtime in cultures containing CAR T cells. Morphometric analyses of the endothelial compartment showed E:T ratio dependent disruption of endothelial vessels. Additionally, this system was able to distinguish EpCAM ScFv-CD28-CD3z and EpCAM ScFv-TM-4-1BB-CD3z CAR T cells killing abilities and was used for studying the effect of immune checkpoint inhibitors and Temozolomide, a DNA targeting drug, on CAR T cell performance. Altogether, this work adds to the available advanced culture techniques for immunotherapy developers by describing a model that is modular, scalable, and suitable for phenotypic and functional characterization of CAR T cells.

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Patterning Fluid Shear Stress Landscapes with Multiphoton Inner Laser Lithography (MILL) for Live Cell Adhesion and Translocation

Lim, Y. J.; Zhang, J.; Lin, H.; Xu, T.; Li, Y.; Zhang, Z.; Hicks, S. M.; Chudinov, I.; Nechipurenko, D. Y.; Gardiner, E. E.; Lee, S.

2022-06-19 bioengineering 10.1101/2022.06.17.496569 medRxiv
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Heterogenous fluid shear stress is known to provide mechanical cues for cell adhesion and translocation. To assemble 3D microstructures using current fabrication methods in a single channel and recapitulate in vivo heterogenous fluid flow would require hours of fabrication and specialized equipment. Inspired by the traditional art form of inside painting, we developed a technique for 3D fabrication of micro-patterned flow channels and mixed in vivo fluid flow in a matter of minutes. We termed this technique Multiphoton Inner Laser Lithography (MILL). We further showed that when combined with adaptive optics, MILL is compatible with both flat and curved channel shapes. MILL recapitulated in vivo tissue topology and 3D fluid flow within tissue stroma (low fluid shear, 0 - 3.5 dynes/cm2) and blood vessel (high fluid shear, 0 - 80 dynes/cm2). We demonstrate fibroblast cell and platelets adhere and translocate differently between laminar flow patterns that are homogenous versus heterogeneous in real time. Parallel strips of MILL channels were assembled for simultaneous platelet function test to quantify the efficacy of an antithrombotic GPVI Fab (~2000 microthrombi per test). The MILL technique can be readily reproduced in vivo fluid flow in minutes and benefit preclinical screening of drug pharmacokinetics. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC="FIGDIR/small/496569v2_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1efbe9eorg.highwire.dtl.DTLVardef@cbab5aorg.highwire.dtl.DTLVardef@15ed255org.highwire.dtl.DTLVardef@42d14e_HPS_FORMAT_FIGEXP M_FIG C_FIG Significant pointsO_LIMILL channels are made from commercially available off the shelf components using a standard multiphoton imaging system C_LIO_LIVarying degrees of in vivo heterogenous laminar flow is shown to directly influence cells translocating on thinly coated collagen surfaces C_LIO_LIParallel strips of MILL channels were assembled for simultaneous platelet function tests (~2000 microthrombi per test). C_LI

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Immune Cells Infiltration of Patient Derived Glioblastoma Cells spheroids in Acoustic Levitation in Bulk Acoustic Wave devices

Mousset, X.; Kuermanbayi, S.; Dupuis, C.; Jeger-Madiot, N.; Delaunay, V.; Ahmed, I.; El-Habr, E. A.; Chneiweiss, H.; Junier, M.-P.; Aider, J.-L.; PEYRIN, J. M.

2025-03-06 bioengineering 10.1101/2025.02.28.640539 medRxiv
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We describe an acoustofluidic device that allows scaffold-free structuration and culture of multi-cellular tumoroids composed of patient-derived glioblastoma cells only or in combination with non-cancerous cell. A PDMS chip of controlled height was created to allow acoustic levitation of cells using a 2 MHz transducer held on top of the chip. Cells are introduced into the chip through a dedicated inlet upstream of the resonant cavity. The specific design of the cavity together with the acoustic field allow the formation of tumoroids of cells in a precise and controlled manner within the levitation chamber. The acoustic and fluidic environment of the device was determined through experiments confronted with numerical simulations. The control of the flow within the chip was optimized to allow long-term culture of tumoroids and injection of cell culture media without disturbing the tumoroids in levitation. The tumoroids can be also structured, with sequential injections of the different cell types. Using microglia, we show that the acoustofluidic device allows the formation and culture in acoustic levitation of tumoroids mixing cancer cells with other cells populating the tumor as well as immune cell infiltration within the tumoroids. These results demonstrate the suitability of acoustofluidic levitation as an original 3D culture method adapted to the exploration of cancer growth at multiple levels.

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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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Spatiotemporal Patterns of Active Deformation Reveal Downregulation of Cell-Cell Adhesion in Patient-Derived Colorectal Cancer Organoids with BRAF Mutation

Nagai, S.; Suzuki, R.; Yamakawa, G.; Fukuda, A.; Seno, H.; Tanaka, M.

2026-03-08 biophysics 10.64898/2026.03.07.710277 medRxiv
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Colorectal cancer (CRC) is the second most common cause of cancer-related mortality. At the molecular level, CRC is associated with genetic mutations and epigenetic modifications that dysregulate various signaling networks. From the biophysical viewpoint, invasive and metastatic cell migration need to be empowered by mechanical forces. In this study, we analyze the dynamic deformation of patient-derived CRC organoids in Fourier space and demonstrate how organoids with protooncogene BRAF mutation exhibit deformation phenotypes at an early stage. The organoids with BRAFmut have significantly lower elasticity and higher viscosity than those with BRAFWT, which mathematically indicated as the weakening of cell-cell adhesion. Immunohistochemical images, qRT-PCR, and TCGA data analysis confirm the downregulation of E-cadherin (CDH1) in BRAFmut organoids as well as in BRAFmut CRC, suggesting that the decrease in cell-cell adhesion in BRAFmut CRC facilitates invasive and metastatic migration. Notably, the recovery of CDH1 expression by pharmacological inhibition of DNA methylation can quantitatively be detected as the change in mechanical properties, suggesting that the complementary combination of dynamic phenotyping, mathematical modelling, and molecular-level analyses has a potential to unravel the mechanistic causality of the critical gene mutation and CRCs prognosis and the response to therapeutic interventions.

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Controlled disturbed flows on the endothelium result in increased inflammation, nuclear lamin disruption and heterochromatin condensation

Paddillaya, N.; Mahulkar, S.; Arakeri, J.; Gundiah, N.

2023-08-28 bioengineering 10.1101/2023.08.27.555040 medRxiv
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Early atherosclerotic lesions often develop in areas of disturbed flow within arterial curvatures and bifurcations. Complex flows alter the signaling of inflammatory and other signaling molecules that may exacerbate the disease phenotype. Microfluidic platforms to assess changes in endothelial mechanobiology generally employ laminar unidirectional or oscillatory flows generated in straight channels; such platforms do not however mimic the complex time-varying bi-directional shear patterns on arterial walls. We fabricated an endothelium-on-chip device to generate "controlled" disturbed flows, characterized using a wall shear rosette, such as those reported in aneurysmal vessels and in regions with atherosclerotic plaques. We cultured human aortic endothelial cells (HAEC) in the device and subjected the monolayer to a circular shear rosette which represents bidirectional and oscillatory shear stresses. Immunofluorescence results show large cuboidal cells with significantly higher nuclear areas, changes in the localization of VE-Cadherin, elevated actin and NF-kB expressions in the device as compared to cell monolayers subjected to laminar flow, unidirectional oscillatory flow, and No-flow conditions. The creation of a dysfunctional endothelial monolayer due to bidirectional oscillatory flows also correlated with dramatic changes to the lamin A/C distribution and heterochromatin organization in the nucleus that have not been reported earlier. Such studies are potentially useful to assess novel therapeutics, mitigate effects of vascular disease for personalized medicine, study thrombus creation in the vicinity of inflamed endothelial monolayers, and reduce ourreliance on animal trials. Our device and analytical method represent the first successful demonstration of generating controlled disturbed flows in microfluidic devices

19
Cyclic stretch regulates epithelial cell migration in a frequency dependent manner via vinculin recruitment to cell-cell contacts

Dow, L. P.; Surace, S.; Morozov, K.; Kennedy, R.; Pruitt, B. L.

2023-08-21 bioengineering 10.1101/2023.08.19.553915 medRxiv
Top 0.1%
5.9%
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Epithelial cell migration is critical in regulating wound healing and tissue development. The epithelial microenvironment is incredibly dynamic, subjected to mechanical cues including cyclic stretch. While cyclic cell stretching platforms have revealed responses of the epithelium such as cell reorientation and gap formation, few studies have investigated the long-term effects of cyclic stretch on cell migration. We measured the migratory response of the epithelium to a range of physiologically relevant frequencies and stretch. We integrated our experimental approach with high-throughput cell segmentation to discover a relationship between changes in cell morphology and migration as a function of cyclic stretch. Our results indicate that lower stretch frequencies (i.e., 0.1 Hz) arrest epithelial migration, accompanied by cell reorientation and high cell shape solidity. We found that this response is also accompanied by increased recruitment of vinculin to cell-cell contacts, and this recruitment is necessary to arrest cell movements. This work demonstrates a critical role for frequency dependence in epithelial response to mechanical stretch. These results confirm the mechanosensitive nature of vinculin within the adherens junction, but independently reveal a novel mechanism of low frequency stress response in supporting epithelial integrity by arresting cell migration.

20
Shear-induced phenotypic transformation of microglia in vitro

Park, E.; Ahn, S. I.; Park, J.-S.; Shin, J. H.

2023-02-22 bioengineering 10.1101/2023.02.21.529442 medRxiv
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5.6%
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Brain cells are influenced by continuous fluid shear stress driven by varying hydrostatic and osmotic pressure conditions, depending on the brains pathophysiological conditions. While all brain cells are sensitive to the subtle changes in various physicochemical factors in the microenvironment, microglia, the resident brain immune cells, exhibit the most dramatic morphodynamic transformation. However, little is known about the phenotypic alterations in microglia in response to the changes in fluid shear stress. In this study, we first established a flow-controlled microenvironment to investigate the effects of shear flow on microglial phenotypes, including morphology, motility, and activation states. Microglia exhibited two distinct morphologies with different migratory phenotypes in a static condition: bipolar cells that oscillate along their long axis and unipolar cells that migrate persistently. When exposed to flow, a significant fraction of bipolar cells showed unstable oscillation with an increased amplitude of oscillation and a decreased frequency, which consequently led to the phenotypic transformation of oscillating cells into migrating cells. Interestingly, the level of pro-inflammatory genes increased in response to shear stress, while there were no significant changes in the level of anti-inflammatory genes. Our findings suggest that an interstitial fluid-level stimulus can cause a dramatic phenotypic shift in microglia toward pro-inflammatory states, shedding light on pathological outbreaks of severe brain diseases. Given that the fluidic environment in the brain can be locally disrupted in pathological circumstances, the mechanical stimulus by a fluid flow should also be considered a crucial element in regulating the immune activities of the microglia in brain diseases. Statement of SignificanceCellular morphology and motility are important factors that encompass the alterations in protein and gene-level expressions within cells. In pathological conditions, microglia, the resident brain immune cells, are known to undergo morphodynamic transformations in response to various physicochemical stimuli. Besides the commonly known soluble biochemical factors in the microenvironment, the differential flow characteristics of ISF have been linked to several neurological diseases, such as Alzheimers, Parkinsons, and brain tumors. Microglial cells, which are extremely sensitive to subtle changes in extracellular stimuli, have been identified as key players in these pathological conditions. Despite its importance, however, it has been challenging to study the sole effect of a shear flow on microglia. We investigated the morphodynamic features of microglia in response to precisely controlled interstitial-level fluid flow conditions using a microfluidic system in which isolated microglia are monitored in real-time while the undesirable effects from other extracellular factors are minimized.