3D cell cultures toward quantitative high-throughput drug screening

Keratin: A potential driver of tumor metastasis

Keratins, as essential components of intermediate filaments in epithelial cells, play a crucial role in maintaining cell structure and function. In various malignant epithelial tumors, abnormal keratin expression is frequently observed and serves not only as a diagnostic marker but also closely correlates with tumor progression. Extensive research has demonstrated that keratins are pivotal in multiple stages of tumor metastasis, including responding to mechanical forces, evading the immune system, reprogramming metabolism, promoting angiogenesis, and resisting apoptosis. Here we emphasize that keratins significantly enhance the migratory and invasive capabilities of tumor cells, making them critical drivers of tumor metastasis. These findings highlight the importance of targeting keratins as a strategic approach to combat tumor metastasis, thereby advancing our understanding of their role in cancer progression and offering new therapeutic opportunities.

High-Throughput Chemotherapeutic Drug Screening System for Gastric Cancer (Cure-GA)

BACKGROUND

Three dimensional (3D) cell cultures can be effectively used for drug discovery and development but there are still challenges in their general application to high-throughput screening. In this study, we developed a novel high-throughput chemotherapeutic 3D drug screening system for gastric cancer, named 'Cure-GA', to discover clinically applicable anticancer drugs and predict therapeutic responses.

METHODS

Primary cancer cells were isolated from 143 fresh surgical specimens by enzymatic treatment. Cell-Matrigel mixtures were automatically printed onto the micropillar surface then stabilized in an optimal culture medium for 3 days to form tumoroids. These tumoroids were exposed in the drug-containing media for 7 days. Cell viability was measured by fluorescence imaging and adenosine triphosphate assays. On average, 0.31 ± 0.23 g of fresh tumor tissue yielded 4.05×106 ± 4.38×106 viable cells per sample.

RESULTS

Drug response results were successfully acquired from 103 gastric cancer tissues (success rate = 72%) within 13 ± 2 days, averaging 6.4 ± 2.7 results per sample. Pearson correlation analysis showed viable cell numbers significantly impacted drug data acquisition (p < 0.00001). Tumoroids retained immunohistochemical characteristics, mutation signatures, and gene expression consistent with primary tumors. Drug reactivity data enabled prediction of synergistic drug correlations. Additionally, a multiparameter index-based prognosis model for patients undergoing gastrectomy followed by adjuvant XELOX was developed, showing significant differences in 1-year recurrence-free survival rates between drug responders and non-responders (p < 0.0001).

CONCLUSIONS

The Cure-GA platform enables rapid evaluation of chemotherapeutic responses using patient-derived tumoroids, providing clinicians with crucial insights for personalized treatment strategies and improving therapeutic outcomes.

Imaging 3D cell cultures with optical microscopy

Three-dimensional (3D) cell cultures have gained popularity in recent years due to their ability to represent complex tissues or organs more faithfully than conventional two-dimensional (2D) cell culture. This article reviews the application of both 2D and 3D microscopy approaches for monitoring and studying 3D cell cultures. We first summarize the most popular optical microscopy methods that have been used with 3D cell cultures. We then discuss the general advantages and disadvantages of various microscopy techniques for several broad categories of investigation involving 3D cell cultures. Finally, we provide perspectives on key areas of technical need in which there are clear opportunities for innovation. Our goal is to guide microscope engineers and biomedical end users toward optimal imaging methods for specific investigational scenarios and to identify use cases in which additional innovations in high-resolution imaging could be helpful.

Development of Sheep Duodenum Intestinal Organoids and Implementation of High-Throughput Screening Platform for Veterinary Applications

New therapeutic molecules for farm animals are needed to address worldwide problems in the food industry, like the rise of resistance among ruminant parasites and pathogenic microbes. Since in vivo testing would involve an excessive number of animals, with consequent ethical and economic issues, the generation of sheep intestinal organoids represents a promising close-to-reality in vitro model for veterinary drug development; however, the characterization and application of such organoids remain limited. In this study, ovine intestinal organoids were generated from adult LGR5+ stem cells from the intestinal crypts of freshly slaughtered lambs, and developed in an in vitro culture system. Morphological analysis via brightfield microscopy and immunocytochemical staining revealed a pseudostratified epithelium with multiple cell types, and distinct apical-basal polarity, while RNA sequencing validated the preservation of the physiological characteristics of the original organ. The development and characterization of a robust and reproducible protocol for culturing sheep duodenum intestinal organoids in a high-throughput screening (HTS) compatible format demonstrated reliability in HTS applications, with Z'-factor tests indicating robust assay performance. Dose-response studies using pre-identified compounds showed comparable pharmacodynamic profiles between mouse and sheep organoids. These findings establish sheep intestinal organoids as an innovative tool for veterinary pharmacology and toxicology, offering a cost-effective and sustainable platform to address challenges such as drug resistance and improve livestock health.

Mechanically regulated microcarriers with stem cell loading for skin photoaging therapy

Long-term exposure to ultraviolet radiation compromises skin structural integrity and results in disruption of normal physiological functions. Stem cells have gained attention in anti-photoaging, while controlling the tissue mechanical microenvironment of cell delivery sites is crucial for regulating cell fate and achieving optimal therapeutic performances. Here, we introduce a mechanically regulated human recombinant collagen (RHC) microcarrier generated through microfluidics, which is capable of modulating stem cell differentiation to treat photoaged skin. By controlling the cross-linking parameters, the mechanical properties of microcarriers could precisely tuned to optimize the stem cell differentiation. The microcarriers are surface functionalized with fibronectin (Fn)-platelet derived growth factor-BB (PDGF-BB) to facilitate adipose derived mesenchymal stem cells (Ad-MSCs) loading. In in vivo experiments, subcutaneous injection of stem cell loaded RHC microcarriers significantly reduced skin wrinkles after ultraviolet-injury, effectively promoted collagen synthesis, and increased vascular density. These encouraging results indicate that the present mechanically regulated microcarriers have great potential to deliver stem cells and regulate their differentiation for anti-photoaging treatments.

Selective activity of Tabebuia avellanedae against Giardia duodenalis infecting organoid-derived human gastrointestinal epithelia

Giardia duodenalis is a widespread intestinal protozoan that affects mammals, including humans. Symptoms can range from being subclinical to causing severe abdominal pain and diarrhoea. Giardiasis often requires repeated treatment with synthetic drugs like metronidazole. In recent years, treatment failures in clinical cases involving nitroimidazoles have been increasingly reported. Consequently, identifying therapeutic alternatives is necessary. Medicinal plants have traditionally been used as antiparasitic compounds, but systematic evaluation under controlled experimental conditions is often lacking. Here, we evaluated the in vitro efficacy of Tabebuia avellanedae dry and hydroalcoholic extracts, as well as one of its active compounds, β-lapachone, as potential treatment against G. duodenalis infection. We observed effective antigiardial activity for all tested compounds, with β-lapachone exhibiting lower IC50 values than metronidazole. Cytotoxic effects often limit therapeutic concentration windows of opportunity, and choosing an informative model to assess them is not straightforward. In the present case, only T. avellanedae hydroalcoholic extract showed no cytotoxicity on tumoral human intestinal Caco-2 cell line, and only a trend of inhibition when tested on canine epithelial kidney MDCK cells. To introduce a more physiological test system, we used in vitro G. duodenalis infection experiments in a trans-well set-up using organoid derived monolayers (ODM) to assess at the same time drug efficacy against the parasite and safety on primary human intestinal epithelia, a likely surrogate for in vivo conditions. Our studies using this model point towards the potential therapeutic opportunity for non-systemic applications of T. avellanedae extracts and a relevant ingredient of these, β-lapachone. The data suggest that ODM co-cultures with G. duodenalis are suitable for testing antigiardial compounds, providing a more informative in vitro model before progressing to in vivo tests.

Dressed in Collagen: 2D and 3D Cardiac Fibrosis Models

Cardiovascular diseases (CVD), the leading cause of death worldwide, and their strong association with fibrosis highlight the pressing need for innovative antifibrotic therapies. In vitro models have emerged as valuable tools for replicating cardiac fibrosis 'in a dish', facilitating the study of disease mechanisms and serving as platforms for drug testing and development. These in vitro systems encompass 2D and 3D models, each with its own limitations and advantages. 2D models offer high reproducibility, cost-effectiveness, and high-throughput capabilities, but they oversimplify the complex fibrotic environment. On the other hand, 3D models provide greater biological relevance but are more complex, harder to reproduce, and less suited for high-throughput screening. The choice of model depends on the specific research question and the stage of drug development. Despite significant progress, challenges remain, including the integration of immune cells in cardiac fibrosis and optimizing the scalability and throughput of highly biomimetic systems. Herein, we review recent in vitro cardiac fibrosis models, with a focus on their shared characteristics and remaining challenges, and explore how in vitro fibrosis models of other organs could inspire novel approaches in cardiac research, showcasing potential strategies that could be adapted to refine myocardial fibrosis models.

Advancing humanized 3D tumor modeling using an open access xeno-free medium

Despite limitations like poor mimicry of the human cell microenvironment, contamination risks, and batch-to-batch variation, cell culture media with animal-derived components such as fetal bovine serum (FBS) have been used in vitro for decades. Moreover, a few reports have used animal-product-free media in advanced high throughput three-dimensional (3D) models that closely mimic in vivo conditions. To address these challenges, we combined a high throughput 3D model with an open access, FBS-free chemically-defined medium, Oredsson Universal Replacement (OUR) medium, to create a more realistic 3D in vitro drug screening system. To reach this goal, we report the gradual adaptation procedure of three cell lines: human HeLa cervical cancer cells, human MCF-7 breast cancer cells, and cancer-associated fibroblasts (CAFs) from FBS-supplemented medium to OUR medium, while closely monitoring cell attachment, proliferation, and morphology. Our data based on cell morphology studies with phase contrast and real-time live imaging demonstrates a successful adaptation of cells to proliferate in OUR medium showing sustained growth kinetics and maintaining population doubling time. The morphological analysis demonstrates that HeLa and MCF-7 cells displayed altered cell morphology, with a more spread-out cytoplasm and significantly lower circularity index, while CAFs remained unaffected when grown in OUR medium. 3D fiber scaffolds facilitated efficient cell distribution and ingrowth when grown in OUR medium, where cells expand and infiltrate into the depths of 3D scaffolds. Drug toxicity evaluation of the widely used anti-cancer drug paclitaxel (PTX) revealed that cells grown in 3D cultures with OUR medium showed significantly lower sensitivity to PTX, which was consistent with the FBS-supplemented medium. We believe this study opens the way and encourages the scientific community to use animal product-free cell culture medium formulations for research and toxicity testing.

Capturing the Heterogeneity of the PDAC Tumor Microenvironment: Novel Triple Co-Culture Spheroids for Drug Screening and Angiogenic Evaluation

Pancreatic ductal adenocarcinoma (PDAC) presents significant treatment challenges due to its desmoplastic reaction, which impedes therapeutic effectiveness, highlighting the need for advanced vitro models to better mimic the complex tumor environment. The current three-dimensional co-culture models of fibroblasts and endothelial cells are lacking, which presents a challenge for performing more comprehensive in vitro research. Our study developed triple co-culture spheroid models using MiaPaCa-2 and BxPC-3 cancer cell lines, with RLT-PSC and hPSC21 pancreatic stellate cell lines and the endothelial cell line HMEC-1. These models were assessed through growth assays, multicolor flow cytometry to optimize cell ratios, cell viability assays to evaluate drug responses, and a tube formation assay with a spheroid-conditioned medium to examine angiogenesis. Our triple co-culture spheroids effectively replicate the PDAC microenvironment, showing significant variations in drug responses influenced by cellular composition, density, and spatial arrangement. The tube formation assay showcased the potential of our models to quantitatively assess a treatment-induced angiogenic response. These cost-effective triple-co-culture in vitro spheroid models provide vital insights into the PDAC microenvironment, significantly improving the quality of the in vitro evaluation of treatment responses.

Retina-on-chip: engineering functional in vitro models of the human retina using organ-on-chip technology

The retina is a complex and highly metabolic tissue in the back of the eye essential for human vision. Retinal diseases can lead to loss of vision in early and late stages of life, significantly affecting patients' quality of life. Due to its accessibility for surgical interventions and its isolated nature, the retina is an attractive target for novel genetic therapies and stem cell-based regenerative medicine. Understanding disease mechanisms and evaluating new treatments require relevant and robust experimental models. Retina-on-chip models are microfluidic organ-on-chip systems based on human tissue that capture multi-cellular interactions and tissue-level functions in vitro. Various retina-on-chip models have been described in literature. Some of them capture basic retinal barrier functions while others replicate key events underlying vision. In addition, some of these cellular systems have also been used in studies to explore their added value in retinal disease modeling. Most existing retina-on-chip models capture limited aspects of the phenotypic complexity of human diseases. This limitation arises primarily from the challenges related to controlled recapitulation of retinal function, including the relevant multi-cellular interactions and functional read-outs. In this review, we provide an update on recent advancements in the field of retina-on-chip, and we discuss the biotechnical strategies to further enhance the physiological relevance of the models. We emphasize that developers and researchers should prioritize the incorporation of the full spectrum of retinal complexity to effectuate a direct impact of retina-on-chip models in disease modeling and development of therapeutic strategies.

High-Throughput Screening of Five Compound Libraries for Anthelmintic Activity and Toxicity Leads to the Discovery of Two Flavonoid Compounds

Gastrointestinal nematode infections (GINs) in ruminants are a major constraint to efficient livestock production worldwide. Currently, only a limited number of anthelmintic drugs are available for the control of these infections, but their widespread use in preventive deworming campaigns and the incorrect administration of the drugs are responsible for the emergence of resistance. Therefore, new anthelmintic drugs are urgently needed. However, drug discovery methods for new anthelmintics based on GINs isolated from ruminants often have low throughput. In this study, a screening of five commercial collections of chemical compounds, including one collection of anti-infective drugs, three plant-based natural product collections, and one collection from the FDA-approved Chinese Pharmacopoeia, with a total of 2228 molecules, have been carried out in a high-throughput format. In the single slot screen, 32 compounds (1.44% success rate) achieved a >70% motility inhibition rate. Of these, 10 are known anthelmintic drugs, while the remaining 22 were tested against Haemonchus contortus and a resistant strain of Teladorsagia circumcincta. Four compounds (two flavonoids, chalcone and trans-chalcone), and two anti-infectives (octenidine and tolfenpyrad), showed anthelmintic activity with EC50 values below 20 µM, and were further tested for their safety against HepG2 spheroids and mouse intestinal organoids. Trans-chalcone and chalcone emerged as promising candidates for future development, showing selective indexes > 5, while tolfenpyrad and octenidine require careful evaluation due to their toxicity profiles.

Biofabricated 3D Intestinal Models as an Alternative to Animal-Based Approaches for Drug Toxicity Assays

BACKGROUND

The main challenge in new drug development is accurately predicting the human response in preclinical models.

METHODS

In this study, we developed three different intestinal barrier models using advanced biofabrication techniques: (i) a manual model containing Caco-2 and HT-29 cells on a collagen bed, (ii) a manual model with a Caco-2/HT-29 layer on a HDFn-laden collagen layer, and (iii) a 3D bioprinted model incorporating both cellular layers. Each model was rigorously tested for its ability to simulate a functional intestinal membrane.

RESULTS

All models successfully replicated the structural and functional aspects of the intestinal barrier. The 3D bioprinted intestinal model, however, demonstrated superior epithelial barrier integrity enhanced tight junction formation, microvilli development, and increased mucus production. When subjected to Ibuprofen, the 3D bioprinted model provided a more predictive response, underscoring its potential as a reliable in vitro tool for drug toxicity testing.

CONCLUSION

Our 3D bioprinted intestinal model presents a robust and predictive platform for drug toxicity assessments, significantly reducing the need for animal testing. This model not only aligns with ethical testing protocols but also offers enhanced accuracy in predicting human responses, thereby advancing the field of drug development.

Revolutionizing cardiovascular research: Human organoids as a Beacon of hope for understanding and treating cardiovascular diseases

Organoids, exhibiting the capability to undergo differentiation in specific in vitro growth environments, have garnered significant attention in recent years due to their capacity to recapitulate human organs with resemblant in vivo structures and physiological functions. This groundbreaking technology offers a unique opportunity to study human diseases and address the limitations of traditional animal models. Cardiovascular diseases (CVDs), a leading cause of mortality worldwide, have spurred an increasing number of researchers to explore the great potential of human cardiovascular organoids for cardiovascular research. This review initiates by elaborating on the development and manufacture of human cardiovascular organoids, including cardiac organoids and blood vessel organoids. Next, we provide a comprehensive overview of their applications in modeling various cardiovascular disorders. Furthermore, we shed light on the prospects of cardiovascular organoids in CVDs therapy, and unfold an in-depth discussion of the current challenges of human cardiovascular organoids in the development and application for understanding and treating CVDs.

Facilitation of Tumor Stroma-Targeted Therapy: Model Difficulty and Co-Culture Organoid Method

Background: Tumors, as intricate ecosystems, comprise oncocytes and the highly dynamic tumor stroma. Tumor stroma, representing the non-cancerous and non-cellular composition of the tumor microenvironment (TME), plays a crucial role in oncogenesis and progression, through its interactions with biological, chemical, and mechanical signals. This review aims to analyze the challenges of stroma mimicry models, and highlight advanced personalized co-culture approaches for recapitulating tumor stroma using patient-derived tumor organoids (PDTOs). Methods: This review synthesizes findings from recent studies on tumor stroma composition, stromal remodeling, and the spatiotemporal heterogeneities of the TME. It explores popular stroma-related models, co-culture systems integrating PDTOs with stromal elements, and advanced techniques to improve stroma mimicry. Results: Stroma remodeling, driven by stromal cells, highlights the dynamism and heterogeneity of the TME. PDTOs, derived from tumor tissues or cancer-specific stem cells, accurately mimic the tissue-specific and genetic features of primary tumors, making them valuable for drug screening. Co-culture models combining PDTOs with stromal elements effectively recreate the dynamic TME, showing promise in personalized anti-cancer therapy. Advanced co-culture techniques and flexible combinations enhance the precision of tumor-stroma recapitulation. Conclusions: PDTO-based co-culture systems offer a promising platform for stroma mimicry and personalized anti-cancer therapy development. This review underscores the importance of refining these models to advance precision medicine and improve therapeutic outcomes.

Strategies to overcome the limitations of current organoid technology - engineered organoids

Organoids, as 3D in vitro models derived from stem cells, have unparalleled advantages over traditional cell and animal models for studying organogenesis, disease mechanisms, drug screening, and personalized diagnosis and treatment. Despite the tremendous progress made in organoid technology, the translational application of organoids still presents enormous challenges due to the complex structure and function of human organs. In this review, the limitations of the translational application of traditional organoid technologies are first described. Next, we explore ways to address many of the limitations of traditional organoid cultures by engineering various dimensions of organoid systems. Finally, we discuss future directions in the field, including potential roles in drug screening, simulated microphysiology system and personalized diagnosis and treatment. We hope that this review inspires future research into organoids and microphysiology system.

Progress in the Application of Organoids-On-A-Chip in Diseases

With the rapid development of the field of life sciences, traditional 2D cell culture and animal models have long been unable to meet the urgent needs of modern biomedical research and new drug development. Establishing a new generation of experimental models and research models is of great significance for deeply understanding human health and disease processes, and developing effective treatment measures. As is well known, long research and development cycles, high risks, and high costs are the "three mountains" facing the development of new drugs today. Organoids and organ-on-chips technology can highly simulate and reproduce the human physiological environment and complex reactions in vitro, greatly improving the accuracy of drug clinical efficacy prediction, reducing drug development costs, and avoiding the defects of drug testing animal models. Therefore, organ-on-chips have enormous potential in medical diagnosis and treatment.

Image processing tools for petabyte-scale light sheet microscopy data

Light sheet microscopy is a powerful technique for high-speed three-dimensional imaging of subcellular dynamics and large biological specimens. However, it often generates datasets ranging from hundreds of gigabytes to petabytes in size for a single experiment. Conventional computational tools process such images far slower than the time to acquire them and often fail outright due to memory limitations. To address these challenges, we present PetaKit5D, a scalable software solution for efficient petabyte-scale light sheet image processing. This software incorporates a suite of commonly used processing tools that are optimized for memory and performance. Notable advancements include rapid image readers and writers, fast and memory-efficient geometric transformations, high-performance Richardson-Lucy deconvolution and scalable Zarr-based stitching. These features outperform state-of-the-art methods by over one order of magnitude, enabling the processing of petabyte-scale image data at the full teravoxel rates of modern imaging cameras. The software opens new avenues for biological discoveries through large-scale imaging experiments.

Novel drug discovery approaches for MMP-13 inhibitors in the treatment of osteoarthritis

Recently, the key role of matrix metalloproteinase-13 (MMP-13) in a variety of diseases has attracted much attention. In the field of osteoarthritis (OA) treatment, the study of MMP-13 inhibitors has become a hotspot, and the development of selective MMP-13 inhibitors is a key direction of OA treatment strategies. This paper aims to summarize the latest research progress on MMP-13 inhibitors in drug design and delivery systems in OA treatment, in order to provide new ideas and strategies for the development of MMP-13 inhibitors. In the context of drug design, researchers have utilized innovative drug discovery strategies to developed a number of potential MMP-13 inhibitors by accurately simulating the active site and analyzing the structure of known inhibitors. With regard to delivery systems, nanotechnology has been extensively employed to enhance the targeting and bioavailability of MMP-13 inhibitors, effectively improving therapeutic efficacy through precise delivery to the lesion site. The latest research developments not only reveal the significant potential of MMP-13 inhibitors in disease treatment, but also provide new directions and challenges for future research.

Patient-derived organoids in precision cancer medicine

Organoids are three-dimensional (3D) cultures, normally derived from stem cells, that replicate the complex structure and function of human tissues. They offer a physiologically relevant model to address important questions in cancer research. The generation of patient-derived organoids (PDOs) from various human cancers allows for deeper insights into tumor heterogeneity and spatial organization. Additionally, interrogating non-tumor stromal cells increases the relevance in studying the tumor microenvironment, thereby enhancing the relevance of PDOs in personalized medicine. PDOs mark a significant advancement in cancer research and patient care, signifying a shift toward more innovative and patient-centric approaches. This review covers aspects of PDO cultures to address the modeling of the tumor microenvironment, including extracellular matrices, air-liquid interface and microfluidic cultures, and organ-on-chip. Specifically, the role of PDOs as preclinical models in gene editing, molecular profiling, drug testing, and biomarker discovery and their potential for guiding personalized treatment in clinical practice are discussed.

Organoids and organoid extracellular vesicles-based disease treatment strategies

Organoids are "mini-organs" that self-organize and differentiate from stem cells under in vitro 3D culture conditions, mimicking the spatial structure and function of tissues in vivo. Extracellular vesicles (EVs) are nanoscale phospholipid bilayer vesicles secreted by living cells, rich in bioactive molecules, with excellent biocompatibility and low immunogenicity. Compared to EVs, organoid-derived EVs (OEVs) exhibit higher yield and enhanced biological functions. Organoids possess stem cell characteristics, and OEVs are capable of delivering active substances, making both highly promising for medical applications. In this review, we provide an overview of the fundamental biological principles of organoids and OEVs, and discuss their current applications in disease treatment. We then focus on the differences between OEVs and traditional EVs. Subsequently, we present methods for the engineering modification of OEVs. Finally, we critically summarize the advantages and challenges of organoids and OEVs. In conclusion, we believe that a deeper understanding of organoids and OEVs will provide innovative solutions to complex diseases.

Development of an automated 3D high content cell screening platform for organoid phenotyping

The use of organoid models in biomedical research has grown substantially since their inception. As they gain popularity among scientists seeking more complex and biologically relevant systems, there is a direct need to expand and clarify potential uses of such systems in diverse experimental contexts. Herein we outline a high-content screening (HCS) platform that allows researchers to screen drugs or other compounds against three-dimensional (3D) cell culture systems in a multi-well format (384-well). Furthermore, we compare the quality of robotic liquid handling with manual pipetting and characterize and contrast the phenotypic effects detected by confocal imaging and biochemical assays in response to drug treatment. We show that robotic liquid handling is more consistent and amendable to high throughput experimental designs when compared to manual pipetting due to improved precision and automated randomization capabilities. We also show that image-based techniques are more sensitive to detecting phenotypic changes within organoid cultures than traditional biochemical assays that evaluate cell viability, supporting their integration into organoid screening workflows. Finally, we highlight the enhanced capabilities of confocal imaging in this organoid screening platform as they relate to discerning organoid drug responses in single-well co-cultures of organoids derived from primary human biopsies and patient-derived xenograft (PDX) models. Altogether, this platform enables automated, imaging-based HCS of 3D cellular models in a non-destructive manner, opening the path to complementary analysis through integrated downstream methods.

A Biomimetic Optical Cardiac Fibrosis-on-a-Chip for High-Throughput Anti-Fibrotic Drug Screening

Cardiac fibrosis has emerged as the primary cause of morbidity, disability, and even mortality in numerous nations. In light of the advancements in precision medicine strategies, substantial attention has been directed toward the development of a practical and precise drug screening platform customized for individual patients. In this study, we introduce a biomimetic cardiac fibrosis-on-a-chip incorporating structural color hydrogels (SCHs) to enable optical high-throughput drug screening. By cocultivating a substantial proportion of cardiac fibroblasts (CFBs) with cardiomyocytes on the SCH, this biomimetic fibrotic microtissue successfully replicates the structural components and biomechanical properties associated with cardiac fibrosis. More importantly, the structural color shift observed in the SCH can be indicative of cardiac contraction and relaxation, making it a valuable tool for evaluating fibrosis progression. By incorporating such fibrotic microtissue into a microfluidic gradient chip, we develop a biomimetic optical cardiac fibrosis-on-a-chip platform that accurately and efficiently screens potential anti-fibrotic drugs. These characteristics suggest that this microphysiological platform possesses the capability to establish a preclinical framework for screening cardiac drugs, and may even contribute to the advancement of precision medicine.

Stem cell-based approaches for developmental neurotoxicity testing

Neurotoxicants are substances that can lead to adverse structural or functional effects on the nervous system. These can be chemical, biological, or physical agents that can cross the blood brain barrier to damage neurons or interfere with complex interactions between the nervous system and other organs. With concerns regarding social policy, public health, and medicine, there is a need to ensure rigorous testing for neurotoxicity. While the most common neurotoxicity tests involve using animal models, a shift towards stem cell-based platforms can potentially provide a more biologically accurate alternative in both clinical and pharmaceutical research. With this in mind, the objective of this article is to review both current technologies and recent advancements in evaluating neurotoxicants using stem cell-based approaches, with an emphasis on developmental neurotoxicants (DNTs) as these have the most potential to lead to irreversible critical damage on brain function. In the next section, attempts to develop novel predictive model approaches for the study of both neural cell fate and developmental neurotoxicity are discussed. Finally, this article concludes with a discussion of the future use of in silico methods within developmental neurotoxicity testing, and the role of regulatory bodies in promoting advancements within the space.

Technological advances and challenges in constructing complex gut organoid systems

Recent advancements in organoid technology have heralded a transformative era in biomedical research, characterized by the emergence of gut organoids that replicate the structural and functional complexity of the human intestines. These stem cell-derived structures provide a dynamic platform for investigating intestinal physiology, disease pathogenesis, and therapeutic interventions. This model outperforms traditional two-dimensional cell cultures in replicating cell interactions and tissue dynamics. Gut organoids represent a significant leap towards personalized medicine. They provide a predictive model for human drug responses, thereby minimizing reliance on animal models and paving the path for more ethical and relevant research approaches. However, the transition from basic organoid models to more sophisticated, biomimetic systems that encapsulate the gut's multifaceted environment-including its interactions with microbial communities, immune cells, and neural networks-presents significant scientific challenges. This review concentrates on recent technological strides in overcoming these barriers, emphasizing innovative engineering approaches for integrating diverse cell types to replicate the gut's immune and neural components. It also explores the application of advanced fabrication techniques, such as 3D bioprinting and microfluidics, to construct organoids that more accurately replicate human tissue architecture. They provide insights into the intricate workings of the human gut, fostering the development of targeted, effective treatments. These advancements hold promise in revolutionizing disease modeling and drug discovery. Future research directions aim at refining these models further, making them more accessible and scalable for wider applications in scientific inquiry and clinical practice, thus heralding a new era of personalized and predictive medicine.

Advancements in 3D In Vitro Models for Colorectal Cancer

The process of drug discovery and pre-clinical testing is currently inefficient, expensive, and time-consuming. Most importantly, the success rate is unsatisfactory, as only a small percentage of tested drugs are made available to oncological patients. This is largely due to the lack of reliable models that accurately predict drug efficacy and safety. Even animal models often fail to replicate human-specific pathologies and human body's complexity. These factors, along with ethical concerns regarding animal use, urge the development of suitable human-relevant, translational in vitro models.

High-Throughput 3D Imaging Flow Cytometry of Suspended Adherent 3D Cell Cultures

3D cell cultures are indispensable in recapitulating in vivo environments. Among the many 3D culture methods, culturing adherent cells on hydrogel beads to form spheroid-like structures is a powerful strategy for maintaining high cell viability and functions in the adherent states. However, high-throughput, scalable technologies for 3D imaging of individual cells cultured on the hydrogel scaffolds are lacking. This study reports the development of a high throughput, scalable 3D imaging flow cytometry platform for analyzing spheroid models. This platform is realized by integrating a single objective fluorescence light-sheet microscopy with a microfluidic device that combines hydrodynamic and acoustofluidic focusing techniques. This integration enabled unprecedentedly high-throughput and scalable optofluidic 3D imaging, processing 1310 spheroids consisting of 28 117 cells min-1. The large dataset obtained enables precise quantification and comparison of the nuclear morphology of adhering and suspended cells, revealing that the adhering cells have smaller nuclei with less rounded surfaces. This platform's high throughput, robustness, and precision for analyzing the morphology of subcellular structures in 3D culture models hold promising potential for various biomedical analyses, including image-based phenotypic screening of drugs with spheroids or organoids.

Recreating chronic respiratory infections in vitro using physiologically relevant models

Despite the need for effective treatments against chronic respiratory infections (often caused by pathogenic biofilms), only a few new antimicrobials have been introduced to the market in recent decades. Although different factors impede the successful advancement of antimicrobial candidates from the bench to the clinic, a major driver is the use of poorly predictive model systems in preclinical research. To bridge this translational gap, significant efforts have been made to develop physiologically relevant models capable of recapitulating the key aspects of the airway microenvironment that are known to influence infection dynamics and antimicrobial activity in vivo In this review, we provide an overview of state-of-the-art cell culture platforms and ex vivo models that have been used to model chronic (biofilm-associated) airway infections, including air-liquid interfaces, three-dimensional cultures obtained with rotating-wall vessel bioreactors, lung-on-a-chips and ex vivo pig lungs. Our focus is on highlighting the advantages of these infection models over standard (abiotic) biofilm methods by describing studies that have benefited from these platforms to investigate chronic bacterial infections and explore novel antibiofilm strategies. Furthermore, we discuss the challenges that still need to be overcome to ensure the widespread application of in vivo-like infection models in antimicrobial drug development, suggesting possible directions for future research. Bearing in mind that no single model is able to faithfully capture the full complexity of the (infected) airways, we emphasise the importance of informed model selection in order to generate clinically relevant experimental data.

Establishment and characterization of two novel patient-derived cell lines from giant cell tumor of bone: NCC-GCTB8-C1 and NCC-GCTB9-C1

Giant cell tumor of bone (GCTB) is a rare osteolytic bone tumor consisting of mononuclear stromal cells, macrophages, and osteoclast-like giant cells. Although GCTB predominantly exhibits benign behavior, the tumor carries a significant risk of high local recurrence. Furthermore, GCTB can occasionally undergo malignant transformation and distal metastasis, making it potentially fatal. The standard treatment is complete surgical resection; nonetheless, an optimal treatment strategy for advanced GCTB remains unestablished, necessitating expanded preclinical research to identify appropriate therapeutic options. However, only one GCTB cell line is publicly available from a cell bank for research use worldwide. The present study reports the establishment of two novel cell lines, NCC-GCTB8-C1 and NCC-GCTB9-C1, derived from the primary tumor tissues of two patients with GCTB. Both cell lines maintained the hallmark mutation in the H3-3A gene, which is associated with tumor formation and development in GCTB. Characterization of these cell lines revealed their steady growth, spheroid-formation capability, and invasive traits. Potential therapeutic agents were identified via extensive drug screening of the two cell lines and seven previously established GCTB cell lines. Among the 214 antitumor agents tested, romidepsin, a histone deacetylase inhibitor, and mitoxantrone, a topoisomerase inhibitor, were identified as potential therapeutic agents against GCTB. Conclusively, the establishment of NCC-GCTB8-C1 and NCC-GCTB9-C1 provides novel and crucial resources that are expected to advance GCTB research and potentially revolutionize treatment strategies.

Magnetic-driven hydrogel microrobots for promoting osteosarcoma chemo-therapy with synthetic lethality strategy

The advancements in the field of micro-robots for drug delivery systems have garnered considerable attention. In contrast to traditional drug delivery systems, which are dependent on blood circulation to reach their target, these engineered micro/nano robots possess the unique ability to navigate autonomously, thereby enabling the delivery of drugs to otherwise inaccessible regions. Precise drug delivery systems can improve the effectiveness and safety of synthetic lethality strategies, which are used for targeted therapy of solid tumors. MYC-overexpressing tumors show sensitivity to CDK1 inhibition. This study delves into the potential of Ro-3306 loaded magnetic-driven hydrogel micro-robots in the treatment of MYC-dependent osteosarcoma. Ro-3306, a specific inhibitor of CDK1, has been demonstrated to suppress tumor growth across various types of cancer. We have designed and fabricated this micro-robot, capable of delivering Ro-3306 precisely to tumor cells under the influence of a magnetic field, and evaluated its chemosensitizing effects, thereby augmenting the therapeutic efficacy and introducing a novel possibility for osteosarcoma treatment. The clinical translation of this method necessitates further investigation and validation. In summary, the Ro-3306-loaded magnetic-driven hydrogel micro-robots present a novel strategy for enhancing the chemosensitivity of MYC-dependent osteosarcoma, paving the way for new possibilities in future clinical applications.

Human patient derived organoids: an emerging precision medicine model for gastrointestinal cancer research

Gastrointestinal cancers account for approximately one-third of the total global cancer incidence and mortality with a poor prognosis. It is one of the leading causes of cancer-related deaths worldwide. Most of these diseases lack effective treatment, occurring as a result of inappropriate models to develop safe and potent therapies. As a novel preclinical model, tumor patient-derived organoids (PDOs), can be established from patients' tumor tissue and cultured in the laboratory in 3D architectures. This 3D model can not only highly simulate and preserve key biological characteristics of the source tumor tissue in vitro but also reproduce the in vivo tumor microenvironment through co-culture. Our review provided an overview of the different in vitro models in current tumor research, the derivation of cells in PDO models, and the application of PDO model technology in gastrointestinal cancers, particularly the applications in combination with CRISPR/Cas9 gene editing technology, tumor microenvironment simulation, drug screening, drug development, and personalized medicine. It also elucidates the ethical status quo of organoid research and the current challenges encountered in clinical research, and offers a forward-looking assessment of the potential paths for clinical organoid research advancement.

Patient-Derived Microphysiological Systems for Precision Medicine

Patient-derived microphysiological systems (P-MPS) have emerged as powerful tools in precision medicine that provide valuable insight into individual patient characteristics. This review discusses the development of P-MPS as an integration of patient-derived samples, including patient-derived cells, organoids, and induced pluripotent stem cells, into well-defined MPSs. Emphasizing the necessity of P-MPS development, its significance as a nonclinical assessment approach that bridges the gap between traditional in vitro models and clinical outcomes is highlighted. Additionally, guidance is provided for engineering approaches to develop microfluidic devices and high-content analysis for P-MPSs, enabling high biological relevance and high-throughput experimentation. The practical implications of the P-MPS are further examined by exploring the clinically relevant outcomes obtained from various types of patient-derived samples. The construction and analysis of these diverse samples within the P-MPS have resulted in physiologically relevant data, paving the way for the development of personalized treatment strategies. This study describes the significance of the P-MPS in precision medicine, as well as its unique capacity to offer valuable insights into individual patient characteristics.

Prediction of Spheroid Cell Death Using Fluorescence Staining and Convolutional Neural Networks

Three-dimensional (3D) cell culture is emerging for drug design and drug screening. Skin toxicity is one of the most important assays for determining the toxicity of a compound before being used in skin application. Much work has been done to find an alternative assay without animal experiments. 3D cell culture is one of the methods that provides clinically relevant models with superior clinical translation compared to that of 2D cell culture. In this study, we developed a spheroid toxicity assay using keratinocyte HaCaT cells with propidium iodide and calcein AM. We also applied the transfer learning-containing convolutional neural network (CNN) to further determine spheroid cell death with fluorescence labeling. Our result shows that the morphologies of the spheroid are the key features in determining the apoptosis cell death of the HaCaT spheroid. Our CNN model provided good statistical measurement in terms of accuracy, precision, and recall in both validation and external test data sets. One can predict keratinocyte spheroid cell death if that spheroid image contains the fluorescence signals from propidium iodide and calcein AM. The CNN model can be accessed in the web application at https://qsarlabs.com/#spheroiddeath.

The adverse outcome pathway for breast cancer: a knowledge management framework bridging biomedicine and toxicology

Breast cancer is the most common cancer worldwide, with an estimated 2.3 million new cases diagnosed every year. Effective measures for cancer prevention and cancer therapy require a detailed understanding of the individual key disease mechanisms involved and their interactions at the molecular, cellular, tissue, organ, and organism level. In that regard, the rapid progress of biomedical and toxicological research in recent years now allows the pursuit of new approaches based on non-animal methods that provide greater mechanistic insight than traditional animal models and therefore facilitate the development of Adverse Outcome Pathways (AOPs) for human diseases. We performed a systematic review of the current state of published knowledge with regard to breast cancer to identify relevant key mechanisms for inclusion into breast cancer AOPs, i.e. decreased cell stiffness and decreased cell adhesion, and to concurrently map non-animal methods addressing these key events. We conclude that the broader sharing of expertise and methods between biomedical research and toxicology enabled by the AOP knowledge management framework can help to coordinate global research efforts and accelerate the transition to advanced non-animal methods, which, when combined into powerful method batteries, closely mimic human physiology and disease states without the need for animal testing.

Cancer organoid-based diagnosis reactivity prediction (CODRP) index-based anticancer drug sensitivity test in ALK-rearrangement positive non-small cell lung cancer (NSCLC)

BACKGROUND

Recently, cancer organoid-based drug sensitivity tests have been studied to predict patient responses to anticancer drugs. The area under curve (AUC) or IC50 value of the dose-response curve (DRC) is used to differentiate between sensitive and resistant patient's groups. This study proposes a multi-parameter analysis method (cancer organoid-based diagnosis reactivity prediction, CODRP) that considers the cancer stage and cancer cell growth rate, which represent the severity of cancer patients, in the sensitivity test.

METHODS

On the CODRP platform, patient-derived organoids (PDOs) that recapitulate patients with lung cancer were implemented by applying a mechanical dissociation method capable of high yields and proliferation rates. A disposable nozzle-type cell spotter with efficient high-throughput screening (HTS) has also been developed to dispense a very small number of cells due to limited patient cells. A drug sensitivity test was performed using PDO from the patient tissue and the primary cancer characteristics of PDOs were confirmed by pathological comparision with tissue slides.

RESULTS

The conventional index of drug sensitivity is the AUC of the DRC. In this study, the CODRP index for drug sensitivity test was proposed through multi-parameter analyses considering cancer cell proliferation rate, the cancer diagnosis stage, and AUC values. We tested PDOs from eight patients with lung cancer to verify the CODRP index. According to the anaplastic lymphoma kinase (ALK) rearrangement status, the conventional AUC index for the three ALK-targeted drugs (crizotinib, alectinib, and brigatinib) did not classify into sensitive and resistant groups. The proposed CODRP index-based drug sensitivity test classified ALK-targeted drug responses according to ALK rearrangement status and was verified to be consistent with the clinical drug treatment response.

CONCLUSIONS

Therefore, the PDO-based HTS and CODRP index drug sensitivity tests described in this paper may be useful for predicting and analyzing promising anticancer drug efficacy for patients with lung cancer and can be applied to a precision medicine platform.

The development and characterization of in vivo-like three-dimensional models of bronchial epithelial cell lines

In vitro models of differentiated respiratory epithelium that allow high-throughput screening are an important tool to explore new therapeutics for chronic respiratory diseases. In the present study, we developed in vivo-like three-dimensional (3-D) models of bronchial epithelial cell lines that are commonly used to study chronic lung disease (16HBE14o-, CFBE41o- and CFBE41o- 6.2 WT-CFTR). To this end, cells were cultured on porous microcarrier beads in the rotating wall vessel (RWV) bioreactor, an optimized suspension culture method that allows higher throughput experimentation than other physiologically relevant models. Cell differentiation was compared to conventional two-dimensional (2-D) monolayer cultures and to the current gold standard in the respiratory field, i.e. air-liquid interface (ALI) cultures. Cellular differentiation was assessed in the three model systems by evaluating the expression and localization of markers that reflect the formation of tight junctions (zonula occludens 1), cell polarity (intercellular adhesion molecule 1 at the apical side and collagen IV expression at the basal cell side), multicellular complexity (acetylated α-tubulin for ciliated cells, CC10 for club cells, keratin-5 for basal cells) and mucus production (MUC5AC) through immunostaining and confocal laser scanning microscopy. Results were validated using Western Blot analysis. We found that tight junctions were expressed in 2-D monolayers, ALI cultures and 3-D models for all three cell lines. All tested bronchial epithelial cell lines showed polarization in ALI and 3-D cultures, but not in 2-D monolayers. Mucus secreting goblet-like cells were present in ALI and 3-D cultures of CFBE41o- and CFBE41o- 6.2 WT-CFTR cells, but not in 16HBE14o- cells. For all cell lines, there were no ciliated cells, basal cells, or club cells found in any of the model systems. In conclusion, we developed RWV-derived 3-D models of commonly used bronchial epithelial cell lines and showed that these models are a valuable alternative to ALI cultures, as they recapitulate similar key aspects of the in vivo parental tissue.

Delivery and Transcriptome Assessment of an In Vitro Three-Dimensional Proximal Tubule Model Established by Human Kidney 2 Cells in Clinical Gelatin Sponges

The high prevalence of kidney diseases and the low identification rate of drug nephrotoxicity in preclinical studies reinforce the need for representative yet feasible renal models. Although in vitro cell-based models utilizing renal proximal tubules are widely used for kidney research, many proximal tubule cell (PTC) lines have been indicated to be less sensitive to nephrotoxins, mainly due to altered expression of transporters under a two-dimensional culture (2D) environment. Here, we selected HK-2 cells to establish a simplified three-dimensional (3D) model using gelatin sponges as scaffolds. In addition to cell viability and morphology, we conducted a comprehensive transcriptome comparison and correlation analysis of 2D and 3D cultured HK-2 cells to native human PTCs. Our 3D model displayed stable and long-term growth with a tubule-like morphology and demonstrated a more comparable gene expression profile to native human PTCs compared to the 2D model. Many missing or low expressions of major genes involved in PTC transport and metabolic processes were restored, which is crucial for successful nephrotoxicity prediction. Consequently, we established a cost-effective yet more representative model for in vivo PTC studies and presented a comprehensive transcriptome analysis for the systematic characterization of PTC lines.

Identification of ATF3 as a novel protective signature of quiescent colorectal tumor cells

Colorectal cancer (CRC) is the third most common cancer and the second leading cause of death in the world. In most cases, drug resistance and tumor recurrence are ultimately inevitable. One obstacle is the presence of chemotherapy-insensitive quiescent cancer cells (QCCs). Identification of unique features of QCCs may facilitate the development of new targeted therapeutic strategies to eliminate tumor cells and thereby delay tumor recurrence. Here, using single-cell RNA sequencing, we classified proliferating and quiescent cancer cell populations in the human colorectal cancer spheroid model and identified ATF3 as a novel signature of QCCs that could support cells living in a metabolically restricted microenvironment. RNA velocity further showed a shift from the QCC group to the PCC group indicating the regenerative capacity of the QCCs. Our further results of epigenetic analysis, STING analysis, and evaluation of TCGA COAD datasets build a conclusion that ATF3 can interact with DDIT4 and TRIB3 at the transcriptional level. In addition, decreasing the expression level of ATF3 could enhance the efficacy of 5-FU on CRC MCTS models. In conclusion, ATF3 was identified as a novel marker of QCCs, and combining conventional drugs targeting PCCs with an option to target QCCs by reducing ATF3 expression levels may be a promising strategy for more efficient removal of tumor cells.

Bone on-a-chip: a 3D dendritic network in a screening platform for osteocyte-targeted drugs

Age-related musculoskeletal disorders, including osteoporosis, are frequent and associated with long lasting morbidity, in turn significantly impacting on healthcare system sustainability. There is therefore a compelling need to develop reliable preclinical models of disease and drug screening to validate novel drugs possibly on a personalized basis, without the need ofin vivoassay. In the context of bone tissue, although the osteocyte (Oc) network is a well-recognized therapeutic target, currentin vitropreclinical models are unable to mimic its physiologically relevant and highly complex structure. To this purpose, several features are needed, including an osteomimetic extracellular matrix, dynamic perfusion, and mechanical cues (e.g. shear stress) combined with a three-dimensional (3D) culture of Oc. Here we describe, for the first time, a high throughput microfluidic platform based on 96-miniaturized chips for large-scale preclinical evaluation to predict drug efficacy. We bioengineered a commercial microfluidic device that allows real-time visualization and equipped with multi-chips by the development and injection of a highly stiff bone-like 3D matrix, made of a blend of collagen-enriched natural hydrogels loaded with hydroxyapatite nanocrystals. The microchannel, filled with the ostemimetic matrix and Oc, is subjected to passive perfusion and shear stress. We used scanning electron microscopy for preliminary material characterization. Confocal microscopy and fluorescent microbeads were used after material injection into the microchannels to detect volume changes and the distribution of cell-sized objects within the hydrogel. The formation of a 3D dendritic network of Oc was monitored by measuring cell viability, evaluating phenotyping markers (connexin43, integrin alpha V/CD51, sclerostin), quantification of dendrites, and responsiveness to an anabolic drug. The platform is expected to accelerate the development of new drug aimed at modulating the survival and function of osteocytes.

Living Anisotropic Structural Color Hydrogels for Cardiotoxicity Screening

Environmental toxins can result in serious and fatal damage in the human heart, while the development of a viable stratagem for assessing the effects of environmental toxins on human cardiac tissue is still a challenge. Herein, we present a heart-on-a-chip based on human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) cultured living anisotropic structural color hydrogels for cardiotoxicity screening. Such anisotropic structural color hydrogels with a conductive parallel carbon nanotube (CNT) upper layer, gelatin methacryloyl (GelMA) interlayer, and inverse opal bottom layer were fabricated by a sandwich replicating approach. The inverse opal structure endowed the anisotropic hydrogels with stable structural color property, while the parallel and conductive CNTs could induce the hiPSC-CMs to grow in a directional manner with consistent autonomous beating. Notably, the resultant hiPSC-CM-cultured hydrogel exhibited synchronous shifts in structural color, responding to contraction and relaxation of hiPSC-CMs, offering a visual platform for monitoring cell activity. Given these features, the hiPSC-CM-cultured living anisotropic structural color hydrogels were integrated into a heart-on-a-chip, which provided a superior cardiotoxicity screening platform for environmental toxins.

Chirality-enhanced transport and drug delivery of graphene nanocarriers to tumor-like cellular spheroid

Chirality, defined as "a mirror image," is a universal geometry of biological and nonbiological forms of matter. This geometry of molecules determines how they interact during their assembly and transport. With the development of nanotechnology, many nanoparticles with chiral geometry or chiroptical activity have emerged for biomedical research. The mechanisms by which chirality originates and the corresponding synthesis methods have been discussed and developed in the past decade. Inspired by the chiral selectivity in life, a comprehensive and in-depth study of interactions between chiral nanomaterials and biological systems has far-reaching significance in biomedicine. Here, we investigated the effect of the chirality of nanoscale drug carriers, graphene quantum dots (GQDs), on their transport in tumor-like cellular spheroids. Chirality of GQDs (L/D-GQDs) was achieved by the surface modification of GQDs with L/D-cysteines. As an in-vitro tissue model for drug testing, cellular spheroids were derived from a human hepatoma cell line (i.e., HepG2 cells) using the Hanging-drop method. Our results reveal that the L-GQDs had a 1.7-fold higher apparent diffusion coefficient than the D-GQDs, indicating that the L-GQDs can enhance their transport into tumor-like cellular spheroids. Moreover, when loaded with a common chemotherapy drug, Doxorubicin (DOX), via π-π stacking, L-GQDs are more effective as nanocarriers for drug delivery into solid tumor-like tissue, resulting in 25% higher efficacy for cancerous cellular spheroids than free DOX. Overall, our studies indicated that the chirality of nanocarriers is essential for the design of drug delivery vehicles to enhance the transport of drugs in a cancerous tumor.

An agarose-alginate microfluidic device for the study of spheroid invasion, ATRA inhibits CAFs-mediated matrix remodeling

Growing evidence demonstrates that cancer-associated fibroblasts (CAF) are responsible for tumor genesis, growth, metastasis, and treatment response. Therefore, targeting these cells may contribute to tumor control. It has been proposed that targeting key molecules and pathways of proliferative functions can be more effective than killing CAFs. In this regard, multicellular aggregates, like spheroids, can be used as human tumor models. Spheroids closely resemble human tumors and mimic many of their features. Microfluidic systems are ideal for cultivation and study of spheroids. These systems can be designed with different biological and synthetic matrices in order to have a more realistic simulation of the tumor microenvironment (TME). In this study, we investigated the effect of all-trans retinoic acid (ATRA) on 3D spheroid invasion of MDA-MB cells exposed to hydrogel matrix derived from CAFs. The number of invasive cells significantly decreased in CAF-ECM hydrogel treated with ATRA (p < 0.05), which indicates that ATRA could be effective for CAFs normalization. This experiment was done using an agarose-alginate microfluidic chip. As compared with common methods, such hydrogel casting is an easier method for chip fabrication and can even reduce costs.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10616-023-00578-y.

On-chip clearing for live imaging of 3D cell cultures

Three-dimensional (3D) cell cultures provide an important model for various biological studies by bridging the gap between two-dimensional (2D) cell cultures and animal tissues. Microfluidics has recently provided controllable platforms for handling and analyzing 3D cell cultures. However, on-chip imaging of 3D cell cultures within microfluidic devices is hindered by the inherent high scattering of 3D tissues. Tissue optical clearing techniques have been used to address this concern but remain limited to fixed samples. As such, there is still a need for an on-chip clearing method for imaging live 3D cell cultures. Here, to achieve on-chip clearing for live imaging of 3D cell cultures, we conceived a simple microfluidic device by integrating a U-shaped concave for culture, parallel channels with micropillars, and differentiated surface treatment to enable on-chip 3D cell culture, clearing, and live imaging with minimal disturbance. The on-chip tissue clearing increased the imaging performance of live 3D spheroids with no influence on cell viability or spheroid proliferation and demonstrated robust compatibility with several commonly used cell probes. It allowed dynamic tracking of lysosomes in live tumor spheroids and enabled quantitative analysis of their motility in the deeper layer. Our proposed method of on-chip clearing for live imaging of 3D cell cultures provides an alternative for dynamic monitoring of deep tissue on a microfluidic device and has the potential to be used in 3D culture-based assays for high-throughput applications.

Multidimensional controllable fabrication of tumor spheroids based on a microfluidic device

Multicellular tumor spheroids (MCTSs) are in vitro solid tumor models with physiological relevance. To achieve robust process control, a MCTS fabrication method that combines cell membrane engineering and droplet microfluidic techniques is designed. The fluidic control and the chemical interactions between biotin and streptavidin enable artificial cell aggregation to be accomplished in seconds. Then, spheroids with a uniform size are fabricated within alginate microcapsules. Microfluidic mixing-based cell aggregation regulates the cell aggregate size and the spheroid composition, and the microcapsules regulate the size of spheroids from 120 to 180 μm. The method shows applicability for various cancer cell lines, including HCT116, HepG2, and A549. In addition, composite colon cancer spheroids consisting of HCT116 and NIH3T3 with predetermined cell ratios and uniform distributions are produced. The generated MCTSs are assessed using the ELISA and UPLC-MS/MS techniques. The release of vascular endothelial growth factor (VEGF) and the 5-fluorouracil (5-FU) resistance differ in the monotypic and cocultured colon cancer models. Our method provides a robust way to produce consistent and customized MCTSs in cancer research and drug screening.

MAC-Seq: Coupling Low-Cost, High-Throughput RNA-Seq with Image-Based Phenotypic Screening in 2D and 3D Cell Models

Transcriptomic profiling has fundamentally influenced our understanding of cancer pathophysiology and response to therapeutic intervention and has become a relatively routine approach. However, standard protocols are usually low-throughput, single-plex assays and costs are still quite prohibitive. With the evolving complexity of in vitro cell model systems, there is a need for resource-efficient high-throughput approaches that can support detailed time-course analytics, accommodate limited sample availability, and provide the capacity to correlate phenotype to genotype at scale. MAC-seq (multiplexed analysis of cells) is a low-cost, ultrahigh-throughput RNA-seq workflow in plate format to measure cell perturbations and is compatible with high-throughput imaging. Here we describe the steps to perform MAC-seq in 384-well format and apply it to 2D and 3D cell cultures. On average, our experimental conditions identified over ten thousand expressed genes per well when sequenced to a depth of one million reads. We discuss technical aspects, make suggestions on experimental design, and document critical operational procedures. Our protocol highlights the potential to couple MAC-seq with high-throughput screening applications including cell phenotyping using high-content cell imaging.

3D Spheroid Invasion Assay for High-Throughput Screening of Small-Molecule Libraries

Cancer metastasis is a complex cascade that involves the activation of cancer cell migration and invasion of the extracellular space. Cancer-associated fibroblasts (CAFs) are known inducers of cancer cell invasion. However, current in vitro invasion assays such as the Boyden chamber assay are cumbersome and low throughput. Therefore, there is an urgent need for new ex vivo, surrogate invasion assays that can faithfully recapitulate the cancer cell invasion process in vitro and are amenable to large-scale screening of small-molecule libraries in a high-throughput fashion. Here, we describe a well-established high-throughput three-dimensional (3D) spheroid invasion assay as a powerful tool to identify novel molecular targets that can potentially mediate CAF-dependent cancer cell invasion.

Functional precision cancer medicine: drug sensitivity screening enabled by cell culture models

Functional precision medicine is a new, emerging area that can guide cancer treatment by capturing information from direct perturbations of tumor-derived, living cells, such as by drug sensitivity screening. Precision cancer medicine as currently implemented in clinical practice has been driven by genomics, and current molecular tumor boards rely extensively on genomic characterization to advise on therapeutic interventions. However, genomic biomarkers can only guide treatment decisions for a fraction of the patients. In this review we provide an overview of the current state of functional precision medicine, highlight advances for drug-sensitivity screening enabled by cell culture models, and discuss how artificial intelligence (AI) can be coupled to functional precision medicine to guide patient stratification.