Modeling Physiological Events in 2D vs. 3D Cell Culture

Induced pluripotent stem cell-related approaches to generate dopaminergic neurons for Parkinson's disease

The progressive loss of dopaminergic neurons in affected patient brains is one of the pathological features of Parkinson's disease, the second most common human neurodegenerative disease. Although the detailed pathogenesis accounting for dopaminergic neuron degeneration in Parkinson's disease is still unclear, the advancement of stem cell approaches has shown promise for Parkinson's disease research and therapy. The induced pluripotent stem cells have been commonly used to generate dopaminergic neurons, which has provided valuable insights to improve our understanding of Parkinson's disease pathogenesis and contributed to anti-Parkinson's disease therapies. The current review discusses the practical approaches and potential applications of induced pluripotent stem cell techniques for generating and differentiating dopaminergic neurons from induced pluripotent stem cells. The benefits of induced pluripotent stem cell-based research are highlighted. Various dopaminergic neuron differentiation protocols from induced pluripotent stem cells are compared. The emerging three-dimension-based brain organoid models compared with conventional two-dimensional cell culture are evaluated. Finally, limitations, challenges, and future directions of induced pluripotent stem cell-based approaches are analyzed and proposed, which will be significant to the future application of induced pluripotent stem cell-related techniques for Parkinson's disease.

Engineering multifunctional surface topography to regulate multiple biological responses

Surface topography or curvature plays a crucial role in regulating cell behavior, influencing processes such as adhesion, proliferation, and gene expression. Recent advancements in nano- and micro-fabrication techniques have enabled the development of biomimetic systems that mimic native extracellular matrix (ECM) structures, providing new insights into cell-adhesion mechanisms, mechanotransduction, and cell-environment interactions. This review examines the diverse applications of engineered topographies across multiple domains, including antibacterial surfaces, immunomodulatory devices, tissue engineering scaffolds, and cancer therapies. It highlights how nanoscale features like nanopillars and nanospikes exhibit bactericidal properties, while many microscale patterns can direct stem cell differentiation and modulate immune cell responses. Furthermore, we discuss the interdisciplinary use of topography for combined applications, such as the simultaneous regulation of immune and tissue cells in 2D and 3D environments. Despite significant advances, key knowledge gaps remain, particularly regarding the effects of topographical cues on multicellular interactions and dynamic 3D contexts. This review summarizes current fabrication methods, explores specific and interdisciplinary applications, and proposes future research directions to enhance the design and utility of topographically patterned biomaterials in clinical and experimental settings.

A microfluidic electrochemical immunosensor for detection of CEA and Ki67 in 3D tumor spheroids

Microfluidic chip-based electrochemical sensors have been developed to detect cancer biomarkers and monitor changes in the tumor microenvironment. However, the limitation of detecting only a single biomarker restricts their utility as accurate diagnostic tools. Simultaneous detection of multiple tumor biomarkers is important for early diagnosis of cancer. In this work, we report the development of a microfluidic-based electrochemical immunosensor platform capable of simultaneously observing multiple biomarkers expressed by three dimensions (3D) cell spheroids. The sensor platform employs a nanocomposite electrode material consisting of gold nanoparticles and carbon nanotubes, which enables sensitive and selective detection. The sensor was fabricated using 3D and printed circuit boards (PCB) printing techniques, demonstrating the feasibility of cost-effective manufacturing. The developed platform was able to quantitatively detect two key cancer biomarkers, carcinoembryonic antigen (CEA) and Ki67, with limits of detection of 0.97 ng/mL for each. Furthermore, the sensor was successfully utilized to observe the knockdown of these biomarkers, showcasing its potential for both diagnostic and therapeutic monitoring applications. These results suggest that the presented electrochemical sensor platform provides a promising lab-on-a-chip technology for comprehensive 3D cell spheroid-based cancer biomarker analysis, which could have significant implications for future clinical diagnostics and personalized medicine.

Interfacial engineering for biomolecule immobilisation in microfluidic devices

Microfluidic devices are used for various applications in biology and medicine. From on-chip modelling of human organs for drug screening and fast and straightforward point-of-care (POC) detection of diseases to sensitive biochemical analysis, these devices can be custom-engineered using low-cost techniques. The microchannel interface is essential for these applications, as it is the interface of immobilised biomolecules that promote cell capture, attachment and proliferation, sense analytes and metabolites or provide enzymatic reaction readouts. However, common microfluidic materials do not facilitate the stable immobilisation of biomolecules required for relevant applications, making interfacial engineering necessary to attach biomolecules to the microfluidic surfaces. Interfacial engineering is performed through various immobilisation mechanisms and surface treatment techniques, which suitably modify the surface properties like chemistry and energy to obtain robust biomolecule immobilisation and long-term storage stability suitable for the final application. In this review, we provide an overview of the status of interfacial engineering in microfluidic devices, covering applications, the role of biomolecules, their immobilisation pathways and the influence of microfluidic materials. We then propose treatment techniques to optimise performance for various biological and medical applications and highlight future areas of development.

Modeling and fabrication of MEW-3D tubular scaffolds with tendon mechanical behavior for tenocyte differentiation

Tendon injuries present substantial challenges in clinical settings, where traditional treatments often lead to suboptimal outcomes, including scar tissue formation, reduced strength, limited range of motion, and re-ruptures. These difficulties primarily arise from the complex hierarchical structure of tendons and their limited healing capacity. Tissue engineering offers promising solutions for tendon regeneration and muscle-to-bone reconnection, typically through the use of biodegradable scaffolds that mimic the extracellular matrix of tendons, thereby supporting cell growth and tissue formation. However, several obstacles must be addressed to develop tendon reconstruction strategies suitable for clinical application. In this study, we developed computational models to design and produce Melt Electrowriting (MEW)-3D tubular structures that replicate the mechanical properties of native mouse Achilles tendons, improving the guidance of tenocyte growth and differentiation. These models incorporated a new approach to consider the non-continuum nature of printed scaffolds formed by sets of fibers interacting with one another. Moreover, these structures facilitated cell confinement, expansion, and alignment, resulting in bundle-like formations with enhanced tensile properties. Importantly, tenocyte differentiation was achieved through a two-step cell culture protocol, which involved transitioning cells from high to low serum media. This approach effectively mitigated the phenotypic drift that often occurs with long-term cell cultures. Statement of Significance Tendon injuries are a common issue in healthcare, often leading to scar tissue, weaker tendons, limited mobility, and frequent re-injury. Tendon engineering aims to address these challenges by using biodegradable "scaffolds" that mimic the natural tendon environment, supporting cell growth and tissue repair. In this study, we developed computational models to design 3D tubular structures using a printing method called Melt Electrowriting (MEW). These structures replicate the mechanical properties of mouse Achilles tendons, guiding tendon cells to grow and differentiate effectively. By creating scaffolds from interwoven fibers, we closely replicated how natural tendon fibers interact, allowing cells to form strong, organized bundles. This approach may improve engineered tendon strength and durability, addressing key challenges in tendon reconstruction strategies.

Matrix Stiffness Regulates the Osteogenic Differentiation of hPDLSCs via DNA Methylation

OBJECTIVES

This study aimed to examine the influence of matrix stiffness on osteogenic differentiation via epigenetic mechanisms in human periodontal ligament stem cells (hPDLSCs), with implications for understanding orthodontic tooth movement.

MATERIALS AND METHODS

hPDLSCs were cultured on substrates with varying stiffness (soft and stiff). Dot blot and immunofluorescence techniques were employed to measure global DNA methylation levels. RT-qPCR and alkaline phosphatase (ALP) activity assays were conducted to assess differences in DNA methylation and osteogenic potential. Additionally, ELISA was used to quantify DNA methyltransferase content and activity.

RESULTS

hPDLSCs on stiffer substrates exhibited increased 5-methylcytosine (5-mC) and higher global DNA methylation levels than those on soft substrates. With increased matrix stiffness, DNMT3A and DNMT3B mRNA expression levels rose. hPDLSCs on stiff matrices also showed elevated DNMT3B enzyme content and osteogenic activity. When global DNA methylation was reduced, mRNA levels of RUNX2, ALP, and Col-1 decreased, along with a notable reduction in ALP staining intensity in the inhibitor group.

CONCLUSIONS

Matrix stiffness is positively associated with global DNA methylation, with DNMT3B likely mediating this regulation in hPDLSCs. Furthermore, DNA methylation levels are positively linked to the osteogenic capability of hPDLSCs.

Adipose derived stem cells - Sources, differentiation capacity and a new target for reconstructive and regenerative medicine

Adipose-derived stem cells (ADSCs) are mesenchymal stem cells (MSCs) derived from adipose tissue with mesenchymal lineage differentiation potential and remarkable potential in regenerative medicine. ADSCs are easily sourced from adipose tissue, share regenerative characteristics akin to other MSCs. Their convenient adherence to plastic culture flasks, coupled with their capacity for in vitro expansion and multi-lineage differentiation, underscores their promise as a robust tool for tissue repair and enhancement. The accessibility of human adipose tissue and the development of minimally invasive isolation protocols have further propelled the autologous use of ADSCs, fueling excitement in both organ repair and regenerative medicine. Consequently, research in ADSCsis experiencing rapid growth. A detailed overview of the current landscape of ADSCs isolation and differentiation capacity including the latest advancements in ADSCs usage, encompassing ongoing clinical investigations are important considerations to understand their potential to shape the landscape of regenerative medicine.

Ketone body 3-hydroxybutyrate mitigates apoptosis and enhances osteogenesis in bone organoid construction via the cAMP/PKA/CREB signaling pathway

Bone organoids offer potential for bone regeneration and in vitro organ models. Current limitations in bone organoid culture systems include low efficiency in construction and functionality, as well as increased apoptosis in prolonged cultures of larger sizes. The ketone body 3-hydroxybutyrate (3HB), synthesized in the liver, addresses these challenges effectively. Our findings suggest that 3HB increases intracellular calcium ion (Ca2+) levels in human bone marrow-derived mesenchymal stem cells (hBMSCs) by activating the hydroxycarboxylic acid receptor 2 (HCAR2). This activation initiates the cAMP/PKA/CREB pathway, which elevates the expression of anti-apoptotic genes such as myeloid cell leukemia 1 (MCL1) and B cell lymphoma 2-related protein A1 (BCL2A1), thereby reducing apoptosis. Furthermore, this pathway boosts the expression of osteogenic proteins, including Runt-related transcription factor 2 (RUNX2) and bone morphogenetic protein 2 (BMP2), facilitating osteogenesis in bone organoids. Consequently, 3HB may enhance the construction of bone organoids that are more mature, larger, and have longer viability.

Engineered epithelial curvature controls Paneth cell localization in intestinal organoids

The cellular organization within organoid models is important to regulate tissue specific function, yet few engineering approaches can control or direct cellular organization. Here, a photodegradable hydrogel is used to create softened regions that direct crypt formation within intestinal organoids, where the dimensions of the photosoftened regions generate predictable and defined crypt architectures. Guided by in vivo metrics of crypt morphology, this photopatterning method is used to control the width and length of in vitro organoid crypts, which ultimately defines the curvature of the epithelium. By tracking expression of differentiated Paneth cell markers in real-time, we show that epithelial curvature directs the localization of Paneth cells within engineered crypts, providing user-directed control over organoid functionality. We anticipate that our improved control over organoid architecture and thus Paneth cell localization will lead to more consistent in vitro organoid models for both mechanistic studies and translational applications.

Interface morphodynamics in living tissues

Interfaces between distinct tissues or between tissues and environments are common in multicellular organisms. The evolution and stability of these interfaces are essential for tissue development, and their dysfunction can lead to diseases such as cancer. Mounting efforts, either theoretical or experimental, have been devoted to uncovering the morphodynamics of tissue interfaces. Here, we review the recent progress of studies on interface morphodynamics. The regulatory mechanisms governing interface evolution are dissected, with a focus on adhesion, cortical tension, cell activity, extracellular matrix, and microenvironment. We examine the methodologies used to study morphodynamics, emphasizing the characteristics of experimental techniques and theoretical models. Finally, we explore the broader implications of interface morphodynamics in tissue morphogenesis and diseases, offering a comprehensive perspective on this rapidly developing field.

The bone microenvironment: new insights into the role of stem cells and cell communication in bone regeneration

Mesenchymal stem cells (MSCs) play a crucial role in bone formation and remodeling. Intrinsic genetic factors and extrinsic environmental cues regulate their differentiation into osteoblasts. Within the bone microenvironment, a complex network of biochemical and biomechanical signals orchestrates bone homeostasis and regeneration. In addition, the crosstalk among MSCs, immune cells, and neighboring cells-mediated by extracellular vesicles and non-coding RNAs (such as circular RNAs and micro RNAs) -profoundly influences osteogenic differentiation and bone remodeling. Recent studies have explored specific signaling pathways that contribute to effective bone regeneration, highlighting the potential of manipulating the bone microenvironment to enhance MSC functionality. The integration of advanced biomaterials, gene editing techniques, and controlled delivery systems is paving the way for more targeted and efficient regenerative therapies. Furthermore, artificial intelligence could improve bone tissue engineering, optimize biomaterial design, and enable personalized treatment strategies. This review explores the latest advancements in bone regeneration, emphasizing the intricate interplay among stem cells, immune cells, and signaling molecules. By providing a comprehensive overview of these mechanisms and their clinical implications, we aim to shed light on future research directions in this rapidly evolving field.

Three-Dimensional-Bioprinted Embedded-Based Cerebral Organoids: An Alternative Approach for Mini-Brain In Vitro Modeling Beyond Conventional Generation Methods

Cerebral organoids (cORGs) obtained from induced pluripotent stem cells (iPSCs) have become significant instruments for investigating human neurophysiology, with the possibility of simulating diseases and enhancing drug discovery. The current approaches require a strict process of manual inclusion in animal-derived matrix Matrigel® and are challenged by unpredictability, operators' skill and expertise, elevated costs, and restricted scalability, impeding their extensive applicability and translational potential. In this study, we present a novel method to generate brain organoids that address these limitations. Our approach does not require a manual, operator-dependent embedding. Instead, it employs a chemically defined hydrogel in which the Matrigel® is diluted in a solution enriched with sodium alginate (SA) and sodium carboxymethylcellulose (CMC) and used as a bioink to print neural embryoid bodies (nEBs). Immunohistochemical, immunofluorescence, and gene expression analyses confirmed that SA-CMC-Matrigel® hydrogel can sustain the generation of iPSC-derived cortical cORGs as the conventional Matrigel®-based approach does. By day 40 of differentiation, hydrogel-based 3D-bioprinted cORGs showed heterogeneous and consistent masses, with a cytoarchitecture resembling an early-stage developmental fetal brain composed of neural progenitor cells PAX6+/Ki67+ organized into tubular structures, and densely packed cell somas with extensive neurites SYP+, suggestive of cortical tissue-like neuronal layer formation.

Angiogenesis: Biological Mechanisms and In Vitro Models

The translation of biomedical devices and drug research is an expensive and long process with a low probability of receiving FDA approval. Developing physiologically relevant in vitro models with human cells offers a solution to not only improving the odds of FDA approval but also to expand our ability to study complex in vivo systems in a simpler fashion. Animal models remain the standard for pre-clinical testing; however, the data from animal models is an unreliable extrapolation when anticipating a human response in clinical trials, thus contributing to the low rates of translation. In this review, we focus on in vitro vascular or angiogenic models because of the incremental role that the vascular system plays in the translation of biomedical research. The first section of this review discusses the most common angiogenic cytokines that are used in vitro to initiate angiogenesis, followed by angiogenic inhibitors where both initiators and inhibitors work to maintain vascular homeostasis. Next, we evaluate previously published in vitro models, where we evaluate capturing the physical environment for biomimetic in vitro modeling. These topics provide a foundation of parameters that must be considered to improve and achieve vascular biomimicry. Finally, we summarize these topics to suggest a path forward with the goal of engineering human in vitro models that emulate the in vivo environment and provide a platform for biomedical device and drug screening that produces data to support clinical translation.

A novel perspective on bone tumors: advances in organoid research

Bone tumor organoids are three-dimensional cell culture models derived from patient tissues or cells, capable of highly replicating the growth patterns and cell interactions of bone tumors in vitro. Current treatments for bone tumors are hindered by challenges such as drug resistance, recurrence, and metastasis. Organoids enhance the physiological relevance of bone tumor models, thereby improving treatment precision and overcoming the limitations of current therapeutic approaches. Organoid technology has made preliminary applications in bone tumor research, including primary bone tumors, metastatic bone tumors, and bone marrow-derived bone tumors. This review will explore the establishment of bone tumor organoids, summarize their applications and prospects in various bone tumor diseases, and discuss their integration with emerging technologies. Additionally, the limitations and future directions of bone tumor organoid research will be discussed. In the future, bone tumor organoids are expected to promote the further development of precision medicine.

A bovine pulmosphere model and multiomics reveal early host response signature in tuberculosis

Early interactions between tubercle bacilli and lung cells are critical in tuberculosis (TB) pathogenesis. Conventional two-dimensional cell cultures fail to replicate the multicellular complexity of lungs. We introduce a three-dimensional pulmosphere model for Mycobacterium tuberculosis infection in bovine systems, demonstrating through comprehensive transcriptome and proteome analyses that these multicellular spheroids closely mimic lung cell diversity, interactions, and extracellular matrix (ECM) composition. Cell viability, hypoxia, and reactive oxygen species assessments over three weeks confirm the model's suitability. To establish infection, we employed M. bovis BCG-an attenuated vaccine strain, and M. tuberculosis H37Rv-a laboratory adapted human clinical strain that is attenuated for cattle infection compared to M. bovis. Both infection upregulated key host pathways; however, M. tuberculosis induced distinct responses, including enhanced ECM receptors expression, neutrophil chemotaxis, interferon signaling, and RIG-1 signaling. A six genes/protein signature- IRF1, CCL5, CXCL8, CXCL10, SERPINE1, and CFB -emerges as an early host response marker to M. tuberculosis infection. Infection with virulent M. bovis and M. orygis revealed a shared upregulated gene signature across Mycobacterium tuberculosis complex species, but with pathogen-specific variations. This study presents a robust ex vivo bovine pulmosphere TB model with implications in biomarkers discovery, high-throughput drug screening, and TB control strategies.

Benzeneboronic acid-modified hyaluronic acid hydrogel enhances the differentiation of dorsal root ganglion stem cells in a three-dimensional environment

Peripheral nerve injuries (PNI) remain challenging to treat due to limited regeneration capacity and the lack of effective therapeutic scaffolds to support nerve repair. This study aims to develop and evaluate a 3-aminophenylboronic acid-modified hyaluronic acid (HAB) hydrogel as a 3D scaffold to enhance Dorsal root ganglion-derived stem cells (DRGSCs) attachment, migration, and neuronal differentiation for peripheral nerve regeneration. The HAB hydrogel was synthesized through an amidation reaction and characterized using Fourier transform infrared spectroscopy (FTIR) and 1H nuclear magnetic resonance (1H NMR). DRGSCs were cultured in HAB hydrogel, and neuronal differentiation was assessed through immunofluorescence staining, PCR, and multi-electrode array (MEA) recordings. Cytotoxicity, proliferation, and in vivo biocompatibility were evaluated through live/dead staining, CCK-8 assays, and subcutaneous implantation in rats. Transcriptomic analysis was performed to explore gene expression profiles. Our results shown that DRGSCs cultured in HAB hydrogel exhibited significantly improved attachment (78.5 % ± 3.2 % vs. 45.3 % ± 2.8 %, p < 0.05) and migration speeds (21.4 μm/h vs. 12.9 μm/h, p < 0.05) compared to 2D cultures. Neuronal differentiation efficiency, as indicated by Tuj1-positive cells, was also higher (72.6 % ± 4.1 % vs. 42.8 % ± 3.9 %, p < 0.01). RNA sequencing identified 990 differentially expressed genes (627 upregulated, 363 downregulated), with pathways involved in synaptic vesicle cycling, glutamatergic and GABAergic synapses significantly enriched (p < 0.05). Validation revealed that the expression trends of Gnao1 and Grm7 in the plastic petri dish and HAB hydrogel groups were consistent with the RNA sequencing results. In vivo, the hydrogel showed excellent biocompatibility, with reduced TNF-α and IL-1β expression over a 28-day degradation cycle (p < 0.01). The HAB hydrogel provides a supportive 3D microenvironment that enhances DRGSCs differentiation and electrophysiological activity, highlighting its potential as a promising scaffold for peripheral nerve regeneration and neuroregenerative medicine.

Gravitational forces and matrix stiffness modulate the invasiveness of breast cancer cells in bioprinted spheroids

The progression of breast cancer is influenced by the stiffness of the extracellular matrix (ECM), which becomes stiffer as cancer advances due to increased collagen IV and laminin secretion by cancer-associated fibroblasts. Intriguingly, breast cancer cells cultivated in two-dimensions exhibit a less aggressive behavior when exposed to weightlessness, or microgravity conditions. This study aims to elucidate the interplay between matrix stiffness and microgravity on breast cancer progression. For this purpose, three-dimensional spheroids of breast cancer cell lines (MCF-7 and MDA-MB-231) were formed. These spheroids were subsequently bioprinted in hydrogels of varying stiffness, obtained by the mixing of gelatin methacrylate and poly(ethylene) glycol diacrylate mixed at different ratios. The constructs were printed with a custom stereolithography (SLA) bioprinter converted from a low-cost, commercially available 3D printer. These bioprinted structures, encapsulating breast cancer spheroids, were then placed in a clinostat (microgravity simulation device) for a duration of seven days. Comparative analyses were conducted between objects cultured under microgravity and standard earth gravity conditions. Protein expression was characterized through fluorescent microscopy, while gene expression of MCF-7 constructs was analyzed via RNA sequencing. Remarkably, the influence of a stiffer ECM on the protein and gene expression levels of breast cancer cells could be modulated and sometimes even reversed in microgravity conditions. The study's findings hold implications for refining therapeutic strategies for advanced breast cancer stages - an array of genes involved in reversing aggressive or even metastatic behavior might lead to the discovery of new compounds that could be used in a clinical setting.

Integration of Organoids With CRISPR Screens: A Narrative Review

Organoids represent a significant advancement in disease modeling, demonstrated by their capacity to mimic the physiological/pathological structure and functional characteristics of the native tissue. Recently CRISPR/Cas9 technology has emerged as a powerful tool in combination with organoids for the development of novel therapies in preclinical settings. This review explores the current literature on applications of pooled CRISPR screening in organoids and the emerging role of these models in understanding cancer. We highlight the evolution of genome-wide CRISPR gRNA library screens in organoids, noting their increasing adoption in the field over the past decade. Noteworthy studies utilizing these screens to investigate oncogenic vulnerabilities and developmental pathways in various organoid systems are discussed. Despite the promise organoids hold, challenges such as standardization, reproducibility, and the complexity of data interpretation remain. The review also addresses the ideas of assessing tumor organoids (tumoroids) against established cancer hallmarks and the potential of studying intercellular cooperation within these models. Ultimately, we propose that organoids, particularly when personalized for patient-specific applications, could revolutionize drug screening and therapeutic approaches, minimizing the reliance on traditional animal models and enhancing the precision of clinical interventions.

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.

Biomimetic Approaches in the Development of Optimised 3D Culture Environments for Drug Discovery in Cardiac Disease

Cardiovascular disease remains the leading cause of death worldwide, yet despite massive investment in drug discovery, the progress of cardiovascular drugs from lab to clinic remains slow. It is a complex, costly pathway from drug discovery to the clinic and failure becomes more expensive as a drug progresses along this pathway. The focus has begun to shift to optimisation of in vitro culture methodologies, not only because these must be undertaken are earlier on in the drug discovery pathway, but also because the principles of the 3Rs have become embedded in national and international legislation and regulation. Numerous studies have shown myocyte cell behaviour to be much more physiologically relevant in 3D culture compared to 2D culture, highlighting the advantages of using 3D-based models, whether microfluidic or otherwise, for preclinical drug screening. This review aims to provide an overview of the challenges in cardiovascular drug discovery, the limitations of traditional routes, and the successes in the field of preclinical models for cardiovascular drug discovery. It focuses on the particular role biomimicry can play, but also the challenges around implementation within commercial drug discovery.

Mechanical Evolution of Metastatic Cancer Cells in 3D Microenvironment

Cellular biomechanics plays a critical role in cancer metastasis and tumor progression. Existing studies on cancer cell biomechanics are mostly conducted in flat 2D conditions, where cells' behavior can differ considerably from those in 3D physiological environments. Despite great advances in developing 3D in vitro models, probing cellular elasticity in 3D conditions remains a major challenge for existing technologies. In this work, optical Brillouin microscopy is utilized to longitudinally acquire mechanical images of growing cancerous spheroids over the period of 8 days. The dense mechanical mapping from Brillouin microscopy enables us to extract spatially resolved and temporally evolving mechanical features that were previously inaccessible. Using an established machine learning algorithm, it is demonstrated that incorporating these extracted mechanical features significantly improves the classification accuracy of cancer cells, from 74% to 95%. Building on this finding, a deep learning pipeline capable of accurately differentiating cancerous spheroids from normal ones solely using Brillouin images have been developed, suggesting the mechanical features of cancer cells can potentially serve as a new biomarker in cancer classification and detection.

Generation of Current Good Manufacturing Practices-Grade Mesenchymal Stromal Cell-Derived Extracellular Vesicles Using Automated Bioreactors

Interest in Current Good Manufacturing Practices (cGMP)-grade extracellular vesicles (EVs) is expanding. Some obstacles in this new but rapidly growing field include a lack of standardization and scalability. This review focuses on automated biomanufacturing of EVs in conditioned media collected from cultured mesenchymal stromal cells (MSCs). Different automated cell culture systems are discussed, including factors affecting EV quantity and quality, isolating EVs manufactured in an automated system, and validations needed. The ultimate goal when manufacturing cGMP-grade EVs is to identify a specific application and characterize the EV population in detail. This is achieved by validating every step of the process, choosing appropriate release criteria, and assuring batch-to-batch consistency. Due to the lack of standards in the field, it is critical to ensure that the cGMP-grade EVs meet FDA standards pertaining to identity, reproducibility, sterility, safety, purity, and potency. A closed-system automated bioreactor can be a valuable tool to generate cGMP-EVs in a scalable, economical, and reproducible manner.

Advanced 3D scaffolds for corneal stroma regeneration: a preclinical progress

Corneal stromal defects represent a significant global cause of blindness, necessitating innovative therapeutic strategies to address the limitations of conventional treatments, such as corneal transplantation. Tissue engineering, a cornerstone of regenerative medicine, offers a transformative approach by leveraging biomaterial-based solutions to restore damaged tissues. Among these, three-dimensional (3D) scaffolds fabricated using advanced techniques like 3D printing have emerged as a promising platform for corneal regeneration. These scaffolds replicate the native extracellular matrix (ECM) architecture, providing a biomimetic microenvironment that supports cell proliferation, differentiation, and tissue integration. This review highlights recent advances in the design and fabrication of 3D scaffolds for corneal stroma engineering (CSE), emphasizing the critical interplay between scaffold architecture, mechanical properties, and bioactive signaling in directing cellular behavior and tissue regeneration. Likewise, we emphasize the diverse range of biomaterials utilized in scaffold fabrication, highlighting their influence on cellular interactions and tissue reconstruction. By elucidating the complex relationship between scaffold design and biologics, this review aims to illuminate the evolution of next-generation strategies for engineering functional corneal tissue. Eventually, this review will provide a comprehensive synthesis of the current state-of-the-art in 3D scaffold-based corneal tissue engineering (CTE), offering insights that could advance progress toward effective vision restoration therapies.

Recent Advances in Hydrogel-Based 3D Disease Modeling and Drug Screening Platforms

Three-dimensional (3D) disease modeling and drug screening systems have become important in tissue engineering, drug screening, and development. The newly developed systems support cell and extracellular matrix (ECM) interactions, which are necessary for the formation of the tissue or an accurate model of a disease. Hydrogels are favorable biomaterials due to their properties: biocompatibility, high swelling capacity, tunable viscosity, mechanical properties, and their ability to biomimic the structure and function of ECM. They have been used to model various diseases such as tumors, cancer diseases, neurodegenerative diseases, cardiac diseases, and cardiovascular diseases. Additive manufacturing approaches, such as 3D printing/bioprinting, stereolithography (SLA), selective laser sintering (SLS), and fused deposition modeling (FDM), enable the design of scaffolds with high precision; thus, increasing the accuracy of the disease models. In addition, the aforementioned methodologies improve the design of the hydrogel-based scaffolds, which resemble the complicated structure and intricate microenvironment of tissues or tumors, further advancing the development of therapeutic agents and strategies. Thus, 3D hydrogel-based disease models fabricated through additive manufacturing approaches provide an enhanced 3D microenvironment that empowers personalized medicine toward targeted therapeutics, in accordance with 3D drug screening platforms.

Enhanced Differentiation of Human Neural Stem Cells into Cortical Neurons Using 3D Chitosan Scaffolds

Human neural stem cells (hNSCs) have the potential to differentiate into various neural cell types, including cortical neurons, which are of particular interest for understanding and treating neurodegenerative diseases. However, traditional 2D culture methods are limited in their ability to accurately mimic the physiologically relevant microenvironment, leading to slow differentiation rates and low yields of mature neurons. In this study, we developed and optimized 3D chitosan scaffolds to promote the more efficient differentiation of hNSCs into cortical neurons. These scaffolds provide a tunable, biocompatible, and mechanically favorable environment, supporting enhanced cell-to-cell interactions and mimicking the extracellular matrix more effectively than 2D systems. The differentiation process was further accelerated by preseeding scaffolds with hNSCs, leading to increased expression of key cortical neuron markers, such as MAP2 and TUBB3, within a 14-day period. Compared to Geltrex-coated controls, the preseeded scaffolds demonstrated superior cell adhesion, viability, and differentiation efficiency, with significant upregulation of mature cortical neuron markers. Our findings suggest that chitosan-based 3D culture systems represent a promising platform for improving the differentiation of hNSCs, offering a faster and more reliable method to generate cortical neurons for neurodegenerative disease research and potential therapeutic applications.

Hydrogen Peroxide-Releasing Hydrogel-Mediated Cellular Senescence Model for Aging Research

Cellular senescence, a process that induces irreversible cell cycle arrest in response to diverse stressors, is a primary contributor to aging and age-related diseases. Currently, exposure to hydrogen peroxide is a widely used technique for establishing in vitro cellular senescence models; however, this traditional method is inconsistent, laborious, and ineffective in vivo. To overcome these limitations, we have developed a hydrogen peroxide-releasing hydrogel that can readily and controllably induce senescence in conventional 2-dimensional cell cultures as well as advanced 3-dimensional microphysiological systems. Notably, we have established 2 platforms using our hydrogen peroxide-releasing hydrogel for investigating senolytics, which is a promising innovation in anti-geronic therapy. Conclusively, our advanced model presents a highly promising tool that offers a simple, versatile, convenient, effective, and highly adaptable technique for inducing cellular senescence. This innovation not only lays a crucial foundation for future research on aging but also markedly accelerates the development of novel therapeutic strategies targeting age-related diseases.

Poly(2-alkyl-2-oxazoline) Hydrogels as Synthetic Matrices for Multicellular Spheroid and Intestinal Organoid Cultures

The extracellular matrix (ECM) plays a crucial role in organoid cultures by supporting cell proliferation and differentiation. A key feature of the ECM is its mechanical influence on the surrounding cells, directly affecting their behavior. Matrigel, the most commonly used ECM, is limited by its animal-derived origin, batch variability, and uncontrollable mechanical properties, restricting its use in 3D cell-model-based mechanobiological studies. Poly(2-alkyl-2-oxazoline) (PAOx) synthetic hydrogels represent an appealing alternative because of their reproducibility and versatile chemistry, enabling tuning of hydrogel stiffness and functionalization. Here, we studied PAOx hydrogels with differing compressive moduli for their potential to support 3D cell growth. PAOx hydrogels support spheroid and organoid growth over several days without the addition of ECM components. Furthermore, we discovered intestinal organoid epithelial polarity reversion in PAOx hydrogels and demonstrate how the tunable mechanical properties of PAOx can be used to study effects on the morphology and oxygenation of live multicellular spheroids.

Three-dimensional tissue platform co-laid with native collagen fibers and cells for phenotypic screening of stem cell interactions

Phenotypic screening of cell-cell and cell-matrix interactions is critical yet challenging for drug discovery and disease modeling. In this study, a scalable 3D tissue platform was developed by co-laying extracted natural insoluble collagen fibers, mesenchymal stem cells, endothelial cells, and neural progenitor cells for phenotypic screening. Cell growth and interactions were enhanced in the co-laid platform, evident through increased cell proliferation, viability, and vascularization. Dense vascular networks rapidly formed through cell-cell and cell-matrix interactions without adding a traditionally needed growth factor set. Both in vitro and implantation studies confirmed that these blood vessels were of human origin. To evaluate the phenotypic screening of cell-cell and cell-matrix interactions, we propose a phenotype screening prototype for stem cell interactions that utilized multivariate analysis encompassing both cell-cell and cell-matrix interactions and demonstrated its effectiveness to screen vasculature formation and autism spectrum disorder (ASD) models. Using the prototype, we confirmed that collagen crosslinking, ROCK, WNT, and YAP pathways impact vasculogenesis. In addition, ASD donor-derived neural progenitor cells can be distinguished from non-ASD control donor-derived neural progenitor cells.

Multi-layered electrode constructs for neural tissue engineering

Although neural tissue engineering holds great therapeutic potential for multiple clinical applications, one important challenge is the development of scaffolds that provide cues required for neural tissue development. To achieve this, biomaterial systems can be leveraged to present appropriate biological, mechanical, topographical and electrical cues that could direct cell fate. In this study, a multi-layered electrode construct was engineered to be used as a platform for 3D cell encapsulation for in vitro applications. The first layer is a conductive hydrogel coating, that improves electrical conductivity from the underlying platinum electrode. The second layer is a biosynthetic hydrogel, specifically tailored to support neural development. This layered electrode construct was electrochemically characterised, and a numerical model was applied to study electrical stimuli reaching the biosynthetic hydrogel layer. The construct was shown to effectively support the growth and proliferation of encapsulated astrocytes within the biosynthetic layer, while the numerical model will enable computational experimentation for benchmarking and study validation. This highly versatile system represents a robust tool to study the influence of electrical stimuli on neural fate, as well as investigating the development of biohybrid interfaces in vitro.

Hydrogels for Cardiac Tissue Regeneration: Current and Future Developments

Myocardial infarction remains a leading cause of death worldwide due to the heart's limited regenerative capability and the current lack of viable therapeutic solutions. Therefore, there is an urgent need to develop effective treatment options to restore cardiac function after a heart attack. Stem cell-derived cardiac cells have been extensively utilised in cardiac tissue regeneration studies. However, the use of Matrigel as a substrate for the culture and maturation of these cells has been a major limitation for the translation of this research into clinical application. Hydrogels are emerging as a promising system to overcome this problem. They are biocompatible and can provide stem cells with a supportive scaffold that mimics the extracellular matrix, which is essential for repairing damaged tissue in the myocardium after an infarction. Thus, hydrogels provide an alternative and reproducible option in addressing myocardial infarction due to their unique potential therapeutic benefits. This review explores the different types of natural and synthetic polymers used to create hydrogels and their various delivery methods, the most common being via injection and cardiac patches and other applications such as bioprinting. Many challenges remain before hydrogels can be used in a clinical setting, but they hold great promise for the future of cardiac tissue regeneration.

Lung-on-a-chip: From design principles to disease applications

To address the growing need for accurate lung models, particularly in light of respiratory diseases, lung cancer, and the COVID-19 pandemic, lung-on-a-chip technology is emerging as a powerful alternative. Lung-on-a-chip devices utilize microfluidics to create three-dimensional models that closely mimic key physiological features of the human lung, such as the air-liquid interface, mechanical forces associated with respiration, and fluid dynamics. This review provides a comprehensive overview of the fundamental components of lung-on-a-chip systems, the diverse fabrication methods used to construct these complex models, and a summary of their wide range of applications in disease modeling and aerosol deposition studies. Despite existing challenges, lung-on-a-chip models hold immense potential for advancing personalized medicine, drug development, and disease prevention, offering a transformative approach to respiratory health research.

Exploring Morphological and Molecular Properties of Different Adipose Cell Models: Monolayer, Spheroids, Gellan Gum-Based Hydrogels, and Explants

White adipose tissue (WAT) plays a crucial role in energy homeostasis and secretes numerous adipokines with far-reaching effects. WAT is linked to diseases such as diabetes, cardiovascular disease, and cancer. There is a high demand for suitable in vitro models to study diseases and tissue metabolism. Most of these models are covered by 2D-monolayer cultures. This study aims to evaluate the performance of different WAT models to better derive potential applications. The stability of adipocyte characteristics in spheroids and two 3D gellan gum hydrogels with ex situ lobules and 2D-monolayer culture is analyzed. First, the differentiation to achieve adipocyte-like characteristics is determined. Second, to evaluate the maintenance of differentiated ASC-based models, an adipocyte-based model, and explants over 3 weeks, viability, intracellular lipid content, perilipin A expression, adipokine, and gene expression are analyzed. Several advantages are supported using each of the models. Including, but not limited to, the strong differentiation in 2D-monolayers, the self-assembling within spheroids, the long-term stability of the stem cell-containing hydrogels, and the mature phenotype within adipocyte-containing hydrogels and the lobules. This study highlights the advantages of 3D models due to their more in vivo-like behavior and provides an overview of the different adipose cell models.

Emerging biotechnologies for engineering liver organoids

The engineering construction of the liver has attracted enormous attention. Organoids, as emerging miniature three-dimensional cultivation units, hold significant potential in the biomimetic simulation of liver structure and function. Despite notable successes, organoids still face limitations such as high variability and low maturity. To overcome these challenges, engineering strategies have been established to maintain organoid stability and enhance their efficacy, laying the groundwork for the development of advanced liver organoids. The present review comprehensively summarizes the construction of engineered liver organoids and their prospective applications in biomedicine. Initially, we briefly present the latest research progress on matrix materials that maintain the three-dimensional morphology of organoids. Next, we discuss the manipulative role of engineering technologies in organoid assembly. Additionally, we outline the impact of gene-level regulation on organoid growth and development. Further, we introduce the applications of liver organoids in disease modeling, drug screening and regenerative medicine. Lastly, we overview the current obstacles and forward-looking perspectives on the future of engineered liver organoids. We anticipate that ongoing innovations in engineered liver organoids will lead to significant advancements in medical applications.

Guidance for evaluating biomaterials' properties and biological potential for dental pulp tissue engineering and regeneration research

BACKGROUND

Dental pulp regeneration is a complex and advancing field that requires biomaterials capable of supporting the pulp's diverse functions, including immune defense, sensory perception, vascularization, and reparative dentinogenesis. Regeneration involves orchestrating the formation of soft connective tissues, neurons, blood vessels, and mineralized structures, necessitating materials with tailored biological and mechanical properties. Numerous biomaterials have entered clinical practice, while others are being developed for tissue engineering applications. The composition and a broad range of material properties, such as surface characteristics, degradation rate, and mechanical strength, significantly influence cellular behavior and tissue outcomes. This underscores the importance of employing robust evaluation methods and ensuring precise and comprehensive reporting of findings to advance research and clinical translation.

AIMS

This article aims to present the biological foundations of dental pulp tissue engineering alongside potential testing methodologies and their advantages and limitations. It provides guidance for developing research protocols to evaluate the properties of biomaterials and their influences on cell and tissue behavior, supporting progress toward effective dental pulp regeneration strategies.

Exploring oncology treatment strategies with tyrosine kinase inhibitors through advanced 3D models (Review)

The limitations of two-dimensional (2D) models in cancer research have hindered progress in fully understanding the complexities of drug resistance and therapeutic failures. However, three-dimensional (3D) models provide a more accurate representation of in vivo environments, capturing critical cellular interactions and dynamics that are essential in evaluating the efficacy and toxicity of tyrosine kinase inhibitors (TKIs). These advanced models enable researchers to explore drug resistance mechanisms with greater precision, optimizing treatment strategies and improving the predictive accuracy of clinical outcomes. By leveraging 3D models, it will be possible to deepen the current understanding of TKIs and drive forward innovations in cancer treatment. The present review discusses the limitations of 2D models and the transformative impact of 3D models on oncology research, highlighting their roles in addressing the challenges of 2D systems and advancing TKI studies.

Pheno-Morphological Screening and Acoustic Sorting of 3D Multicellular Aggregates Using Drop Millifluidics

Three-dimensional multicellular aggregates (MCAs) like organoids and spheroids have become essential tools to study the biological mechanisms involved in the progression of diseases. In cancer research, they are now widely used as in vitro models for drug testing. However, their analysis still relies on tedious manual procedures, which hinders their routine use in large-scale biological assays. Here, a novel drop millifluidic approach is introduced to screen and sort large populations containing over one thousand MCAs: ImOCAS (Image-based Organoid Cytometry and Acoustic Sorting). This system utilizes real-time image processing to detect pheno-morphological traits in MCAs. They are then encapsulated in millimetric drops, actuated on-demand using the acoustic radiation force. The performance of ImOCAS is demonstrated by sorting spheroids with uniform sizes from a heterogeneous population, and by isolating organoids from spheroids with different phenotypes. This approach lays the groundwork for high-throughput screening and high-content analysis of MCAs with controlled morphological and phenotypical properties, which promises accelerated progress in biomedical research.

Study Models for Chlamydia trachomatis Infection of the Female Reproductive Tract

Chlamydia trachomatis (Ct) is a leading cause of sexually transmitted infections globally, often resulting in inflammatory disorders, ectopic pregnancies, and infertility. Studying Ct's pathogenesis remains challenging due to its unique life cycle and host-specific interactions, which require diverse experimental models. Animal studies using mouse, guinea pig, pig, and non-human primate models provide valuable insights into immune responses, hormonal influences, and disease progression. However, they face limitations in terms of translational relevance due to physiological differences, as well as ethical concerns. Complementing these, in vitro systems, ranging from simple monolayer to advanced three-dimensional models, exhibit improved physiological relevance by replicating the human tissue architecture. This includes the detailed investigation of epithelial barrier disruptions, epithelium-stroma interactions, and immune responses at a cellular level. Nonetheless, in vitro models fall short in mimicking the intricate tissue structures found in vivo and, therefore, cannot faithfully replicate the host-pathogen interactions or infection dynamics observed in living organisms. This review presents a comprehensive overview of the in vivo and in vitro models employed over the past few decades to investigate Ct and its pathogenesis, addressing their strengths and limitations. Furthermore, we explore emerging technologies, including organ-on-chip and in silico models, as promising tools to overcome the existing challenges and refine our understanding of Ct infections.

Cholesterol-mediated Lysosomal Dysfunction in APOE4 Astrocytes Promotes α-Synuclein Pathology in Human Brain Tissue

The pathological hallmark of neurodegenerative disease is the aberrant post-translational modification and aggregation of proteins leading to the formation of insoluble protein inclusions. Genetic factors like APOE4 are known to increase the prevalence and severity of tau, amyloid, and α-Synuclein inclusions. However, the human brain is largely inaccessible during this process, limiting our mechanistic understanding. Here, we developed an iPSC-based 3D model that integrates neurons, glia, myelin, and cerebrovascular cells into a functional human brain tissue (miBrain). Like the human brain, we found pathogenic phosphorylation and aggregation of α-Synuclein is increased in the APOE4 miBrain. Combinatorial experiments revealed that lipid-droplet formation in APOE4 astrocytes impairs the degradation of α-synuclein and leads to a pathogenic transformation that seeds neuronal inclusions of α-Synuclein. Collectively, this study establishes a robust model for investigating protein inclusions in human brain tissue and highlights the role of astrocytes and cholesterol in APOE4-mediated pathologies, opening therapeutic opportunities.

Biofabricated tissue model for determining biocompatibility of metallic coatings

Metallic biomaterials are extensively used in orthopedics and dentistry, either as implants or coatings. In both cases, metal ions come into contact with surrounding tissues causing a particular cell response. Here, we present a biofabricated in vitro tissue model, consisting of a hydrogel reinforced with a melt electrowritten mesh, to study the effects of bound and released metal ions on surrounding cells embedded in a hydrogel matrix. We evaluate the biocompatibility, bioactivity, and antibacterial properties of these metal coatings. Our approach involves integrating physical vapour deposition coating technology with 3D bioprinting methods. To produce tissue models, melt electrowritten (MEW) meshes composed of polycaprolactone (PCL) were printed and integrated into cell-laden methacrylated galatin (GelMa). The mouse embryonic fibroblast cell line (NIH3T3) was used. GelMa concentration and printing parameters for MEW were adjusted and mechanical analysis of the models was performed to find the optimal material composition. Optimized models were placed on the glass slide surfaces coated with typically non-toxic metals, i.e. titanium (Ti), tantalum (Ta), zirconium (Zr), silver (Ag), tungsten (W), and niobium (Nb). Except for W, all other coatings were stable in a physiological wet environment, as studied by SEM. The viability of the cells at different distances from the coated surface was analyzed. Antibacterial tests against pathogens Staphylococcus aureus and Escherichia coli were used to assess the models' resistance, important for infection control. While Ag coatings showed toxicity, Nb, Ta, Ti, and Zr coatings promoted fibroblast growth, with the highest cell viability after 14 days of culture revealed for Ta and Nb. The strongest antimicrobial effect against E. coli and S. aureus was observed for Ag and W, while Ta exhibited antibacterial activity only against S. aureus. From a broader perspective, our work offers an effective 3D in vitro model for an in-depth characterization of the biocompatibility of metals and metal coatings.

Triplicate Dynamic Cell Culture Platform for Enhanced Reproducibility in Anti-Cancer Drug Testing

The development of stable and standardized in vitro cytotoxicity testing models is essential for drug discovery and personalized medicine. Microfluidic technologies, recognized for their small size, reduced reagent consumption, and control over experimental variables, have gained considerable attention. However, challenges associated with external pumps, particularly inconsistencies between individual pumping systems, have limited the real-world application of cancer-on-a-chip technology. This study introduces a novel triplicate cell culture system (Tri-CS) that simultaneously supports dynamic cultures in three independent units using a single peristaltic pump, ensuring consistent flow conditions. Our findings demonstrate that the Tri-CS significantly reduces variability compared to individual pump systems, enhancing the reliability of anticancer drug cytotoxicity testing. Furthermore, we evaluated gemcitabine cytotoxicity, which shows enhanced drug efficacy in dynamic conditions. Fluorescein diffusion tests revealed greater diffusion efficiency in dynamic cultures, which contributed to the higher observed drug efficacy. The potential for broader application of the Tri-CS, including its compatibility with commercially available transwells and the opportunity for use in more complex cancer-on-chip models, positions this system as a valuable tool for advancing microphysiological systems in preclinical research.

Rescuing DNMT1 fails to fully reverse the molecular and functional repercussions of its loss in mouse embryonic stem cells

Epigenetic mechanisms are crucial for developmental programming and can be disrupted by environmental stressors, increasing susceptibility to disease. This has sparked interest in therapies for restoring epigenetic balance, but it remains uncertain whether disordered epigenetic mechanisms can be fully corrected. Disruption of DNA methyltransferase 1 (DNMT1), responsible for DNA methylation maintenance, has particularly devastating biological consequences. Therefore, here we explored if rescuing DNMT1 activity is sufficient to reverse the effects of its loss utilizing mouse embryonic stem cells. However, only partial reversal could be achieved. Extensive changes in DNA methylation, histone modifications, and gene expression were detected, along with transposable element derepression and genomic instability. Reduction of cellular size, complexity, and proliferation rate were observed, as well as lasting effects in germ layer lineages and embryoid bodies. Interestingly, by analyzing the impact on imprinted regions, we uncovered 20 regions exhibiting imprinted-like signatures. Notably, while many permanent effects persisted throughout Dnmt1 inactivation and rescue, others arose from the rescue intervention. Lastly, rescuing DNMT1 after differentiation initiation worsened outcomes, reinforcing the need for early intervention. Our findings highlight the far-reaching functions of DNMT1 and provide valuable perspectives on the repercussions of epigenetic perturbations during early development and the challenges of rescue interventions.

Spatially controlled multicellular differentiation of stem cells using triple factor-releasing metal-organic framework-coated nanoline arrays

Improved in vitro models are needed for regenerative therapy and drug screening. Here, we report on functionally aligned nanoparticle-trapped nanopattern arrays for spatially controlled, precise mesenchymal stem cell differentiation on a single substrate. The arrays comprise nanohole and nanoline arrays fabricated through interference lithography and selectively capture of UiO-67 metal-organic frameworks on nanoline arrays with a 99.8% efficiency using an optimised asymmetric spin-coating method. The UiO-67 metal-organic frameworks contain three osteogenic differentiation factors for sustained release over four weeks. The combination of differentiation factors and patterned array allows for generation of adipocytes, osteoblasts, and adipocyte-osteoblast mixtures on nanohole arrays, nanoline arrays, and at the nanohole-nanoline interface, respectively, with mature osteoblasts exhibiting higher marker expression and mineralisation. The sustained release patterned array holds potential for constructing advanced therapeutic and disease state in vitro cellular models.

A systematic review on the culture methods and applications of 3D tumoroids for cancer research and personalized medicine

Cancer is a highly heterogeneous disease, and thus treatment responses vary greatly between patients. To improve therapy efficacy and outcome for cancer patients, more representative and patient-specific preclinical models are needed. Organoids and tumoroids are 3D cell culture models that typically retain the genetic and epigenetic characteristics, as well as the morphology, of their tissue of origin. Thus, they can be used to understand the underlying mechanisms of cancer initiation, progression, and metastasis in a more physiological setting. Additionally, co-culture methods of tumoroids and cancer-associated cells can help to understand the interplay between a tumor and its tumor microenvironment. In recent years, tumoroids have already helped to refine treatments and to identify new targets for cancer therapy. Advanced culturing systems such as chip-based fluidic devices and bioprinting methods in combination with tumoroids have been used for high-throughput applications for personalized medicine. Even though organoid and tumoroid models are complex in vitro systems, validation of results in vivo is still the common practice. Here, we describe how both animal- and human-derived tumoroids have helped to identify novel vulnerabilities for cancer treatment in recent years, and how they are currently used for precision medicine.

The Mucilage From the Opuntia ficus-indica (L.) Mill. Cladodes Plays an Anti-Inflammatory Role in the LPS-Stimulated HepG2 Cells: A Combined In Vitro and In Silico Approach

The effect of a mucilage extracted from Opuntia ficus-indica (L.) Mill (OFI) cladodes was tested in lipopolysaccharide (LPS)-challenged HepG2 hepatocarcinoma cells, through a combined in vitro-in silico approach. The OFI mucilage was characterized by gas chromatography-mass spectrometry and liquid chromatography-high resolution mass spectrometry. In cells treated with OFI (5-10 µg/mL) prior to LPS (1 µg/mL, 24 h), the gene expression profile of pro-inflammatory mediators, namely tumor necrosis factor alpha, interleukin-1 beta, interleukin-8, and cyclo-oxygenase-2, was significantly (p < 0.01) reduced if compared to single LPS-challenged cells. The OFI-mediated cytokines reduction was also validated in polystyrene scaffold-grown 3D HepG2 cultures, undergoing treatment with the OFI mucilage (50 µg/mL, 24 h) and LPS stimulation (50 µg/mL, 24 h). We further demonstrated that OFI suppresses the LPS-triggered inflammatory response via impairment of the Toll-like receptor 4 (TLR4)/Myeloid differentiation protein-88/Nuclear factor-kappa B (NF-kB) pathway, by interfering with NF-kB phosphorylation at Serine 536. By molecular docking approach, we provided in silico demonstration of the direct molecular interaction between the mucilage monosaccharides and the TLR4 that interferes with the LPS receptor binding and down-stream inflammatory cascade activation. We also demonstrated that OFI cladodes mucilage downregulates the TLR4 pathway, showing an anti-inflammatory potential in HepG2 cells.

Advancing Radiobiology: Investigating the Effects of Photon, Proton, and Carbon-Ion Irradiation on PANC-1 Cells in 2D and 3D Tumor Models

Introduction: Pancreatic cancer (PC) is one of the most aggressive and lethal malignancies, calling for enhanced research. Pancreatic ductal adenocarcinoma (PDAC) represents 70-80% of all cases and is known for its resistance to conventional therapies. Carbon-ion radiotherapy (CIRT) has emerged as a promising approach due to its ability to deliver highly localized doses and unique radiobiological properties compared to X-rays. In vitro radiobiology has relied on two-dimensional (2D) cell culture models so far; however, these are not sufficient to replicate the complexity of the in vivo tumor architecture. Three-dimensional (3D) models become a paradigm shift, surpassing the constraints of traditional models by accurately re-creating morphological, histological, and genetic characteristics as well as the interaction of tumour cells with the microenvironment. Materials and Methods: This study investigates the survival of pancreatic cancer cells in both 2D and spheroids, a 3D model, following photon, proton, and carbon-ion irradiation by means of clonogenic, MTT, spheroid growth, and vitality assays. Results: Our results demonstrate that carbon ions are more efficient in reducing cancer cell survival compared to photons and protons. In 2D cultures, carbon-ion irradiation reduced cell survival to approximately 15%, compared to 45% with photons and 30% with protons. In the 3D culture model, spheroid growth was similarly inhibited by carbon-ion irradiation; however, the overall survival rates were higher across all irradiation modalities compared to the 2D cultures. Carbon ions consistently showed the highest efficacy in reducing cell viability in both models. Conclusions: Our research highlights the pivotal role of 3D models in unraveling the complexities of pancreatic cancer radiobiology, offering new avenues for designing more effective and precise treatment protocols.

Substrate stiffness dictates unique doxorubicin-induced senescence-associated secretory phenotypes and transcriptomic signatures in human pulmonary fibroblasts

Cells are subjected to dynamic mechanical environments which impart forces and induce cellular responses. In age-related conditions like pulmonary fibrosis, there is both an increase in tissue stiffness and an accumulation of senescent cells. While senescent cells produce a senescence-associated secretory phenotype (SASP), the impact of physical stimuli on both cellular senescence and the SASP is not well understood. Here, we show that mechanical tension, modeled using cell culture substrate rigidity, influences senescent cell markers like SA-β-gal and secretory phenotypes. Comparing human primary pulmonary fibroblasts (IMR-90) cultured on physiological (2 kPa), fibrotic (50 kPa), and plastic (approximately 3 GPa) substrates, followed by senescence induction using doxorubicin, we identified unique high-stiffness-driven secretory protein profiles using mass spectrometry and transcriptomic signatures, both showing an enrichment in collagen proteins. Consistently, clusters of p21 + cells are seen in fibrotic regions of bleomycin induced pulmonary fibrosis in mice. Computational meta-analysis of single-cell RNA sequencing datasets from human interstitial lung disease confirmed these stiffness SASP genes are highly expressed in disease fibroblasts and strongly correlate with mechanotransduction and senescence-related pathways. Thus, mechanical forces shape cell senescence and their secretory phenotypes.

SenPred: a single-cell RNA sequencing-based machine learning pipeline to classify deeply senescent dermal fibroblast cells for the detection of an in vivo senescent cell burden

BACKGROUND

Senescence classification is an acknowledged challenge within the field, as markers are cell-type and context dependent. Currently, multiple morphological and immunofluorescence markers are required. However, emerging scRNA-seq datasets have enabled an increased understanding of senescent cell heterogeneity.

METHODS

Here we present SenPred, a machine-learning pipeline which identifies fibroblast senescence based on single-cell transcriptomics from fibroblasts grown in 2D and 3D.

RESULTS

Using scRNA-seq of both 2D and 3D deeply senescent fibroblasts, the model predicts intra-experimental fibroblast senescence to a high degree of accuracy (> 99% true positives). Applying SenPred to in vivo whole skin scRNA-seq datasets reveals that cells grown in 2D cannot accurately detect fibroblast senescence in vivo. Importantly, utilising scRNA-seq from 3D deeply senescent fibroblasts refines our ML model leading to improved detection of senescent cells in vivo. This is context specific, with the SenPred pipeline proving effective when detecting senescent human dermal fibroblasts in vivo, but not the senescence of lung fibroblasts or whole skin.

CONCLUSIONS

We position this as a proof-of-concept study based on currently available scRNA-seq datasets, with the intention to build a holistic model to detect multiple senescent triggers using future emerging datasets. The development of SenPred has allowed for the detection of an in vivo senescent fibroblast burden in human skin, which could have broader implications for the treatment of age-related morbidities. All code for the SenPred pipeline is available at the following URL: https://github.com/bethk-h/SenPred_HDF .

Exploring the effects of gut microbiota on cholangiocarcinoma progression by patient-derived organoids

BACKGROUND

Recent research indicates a role of gut microbiota in development and progression of life-threatening diseases such as cancer. Carcinomas of the biliary ducts, the so-called cholangiocarcinomas, are known for their aggressive tumor biology, implying poor prognosis of affected patients. An impact of the gut microbiota on cholangiocarcinoma development and progression is plausible due to the enterohepatic circulation and is therefore the subject of scientific debate, however evidence is still lacking. This review aimed to discuss the suitability of complex cell culture models to investigate the role of gut microbiota in cholangiocarcinoma progression.

MAIN BODY

Clinical research in this area is challenging due to poor comparability of patients and feasibility reasons, which is why translational models are needed to understand the basis of tumor progression in cholangiocarcinoma. A promising approach to investigate the influence of gut microbiota could be an organoid model. Organoids are 3D cell models cultivated in a modifiable and controlled condition, which can be grown from tumor tissue. 3D cell models are able to imitate physiological and pathological processes in the human body and thus contribute to a better understanding of health and disease.

CONCLUSION

The use of complex cell cultures such as organoids and organoid co-cultures might be powerful and valuable tools to study not only the growth behavior and growth of cholangiocarcinoma cells, but also the interaction with the tumor microenvironment and with components of the gut microbiota.

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.

Organoids in skin wound healing

Stem cells (SCs) can self-replicate and differentiate into multiple lineages. Organoids, 3D cultures derived from SCs, can replicate the spatial structure and physiological characteristics of organs in vitro. Skin organoids can effectively simulate the physiological structure and function of skin tissue, reliably restoring the natural skin ecology in various in vitro environments. Skin organoids have been employed extensively in skin development and pathology research, offering valuable insights for drug screening. Moreover, they play crucial roles in skin regeneration and tissue repair. This in-depth review explores the construction and applications of skin organoids in wound healing, with a focus on their construction process, including skin appendage integration, and significant advancements in wound-healing research.