3D Cultures and Organ-on-a-Chip in Cell and Tissue Cultures

A special issue of Cells (ISSN 2073-4409). This special issue belongs to the section "Cell Methods".

Deadline for manuscript submissions: 25 October 2025 | Viewed by 7935

Special Issue Editors


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Department of Bioscience and Agro-Food and Environmental Technology, University of Teramo, via Renato Balzarini 1, 64100 Teramo, Italy
Interests: cell biology; biology of stem cells; biology of reproduction; ovarian angiogenesis; signal transduction; molecular biology; tissue regeneration; regenerative medicine; cancer; histology
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E-Mail Website
Guest Editor
Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, via Renato Balzarini 1, 64100 Teramo, Italy
Interests: cell biology; biology of amniotic derived stem cells; tissue regeneration; regenerative medicine; biology of reproduction; ovarian angiogenesis; signal transduction; molecular biology; advanced reproductive biotechnology techniques
Special Issues, Collections and Topics in MDPI journals

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Guest Editor

Special Issue Information

Dear Colleagues,

Our Special Issue “3D Cultures and Organ-on-a-Chip in Cell and Tissue Cultures” will highlight the transformative shift in tissue engineering and regenerative medicine. This evolution addresses the limitations of traditional two-dimensional (2D) cell culture models, which often fail to replicate the complex physiological environments of living organisms. In contrast, three-dimensional (3D) cell culture methods and organ-on-a-chip technologies provide advanced platforms that closely mimic in vivo conditions, enhancing cellular behavior, differentiation, and interaction.

Furthermore, organ-on-a-chip platforms combine microfluidic technology and living cells to replicate organ-specific microenvironments, allowing for more accurate research on toxicity, physiology, and pharmacological reactions. Drug discovery and illness research are accelerated through the combination of 3D cultures and organ-on-a-chip technologies, which opens up new possibilities for customized treatment. In this context, in recent decades, several models using different organs (lungs on a chip, liver on a chip, kidney on a chip, heart on a chip, intestine on a chip, and skin on a chip) have been successfully developed. However, relatively little research has been carried out on a number of other organs (such as the retina, placenta, and ovaries).

These new techniques have seen increasing implications in virtually all fields in biotechnology, in particular, regenerative medicine, providing a wealth of opportunities, including drug toxicity and efficacy studies, in vitro analyses of biochemicals, and pathogenesis studies on diseases and metabolic activities in cells, in human and veterinary medicine, contributing to the investigation of both basic and application issues.

Thus, for this Special Issue, we welcome the submission of original articles, reviews and mini-reviews, method papers, brief research reports, and perspectives that illustrate and simulate the growing efforts to achieve the convergence of 3D cultures and organ-on-a-chip technologies for new opportunities for regenerative medicine, tissue engineering, and personalized medicine. These technologies could accelerate drug development and disease research while reducing our reliance on animal models, providing new insights and future trends in these rapidly evolving fields.

Prof. Dr. Annunziata Mauro
Prof. Dr. Barbara Barboni
Dr. Giovanna Della Porta
Guest Editors

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Keywords

  • three-dimensional cell culture
  • organ-on-a-chip
  • tissue engineering
  • regenerative medicine
  • drug testing
  • microfluidics
  • in vitro models
  • personalized medicine
  • cellular interaction
  • disease modeling

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Published Papers (4 papers)

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Research

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18 pages, 7099 KB  
Article
Dental Pulp Stem Cell-Derived Organoids: Advancing the Development of 3D Structures
by Loreto Lancia, Fanny Pulcini, Emanuela Mari, Luca Piccoli, Leda Assunta Biordi, Luciano Mutti, Claudio Festuccia, Giovanni Luca Gravina, Vincenzo Mattei, Annunziata Mauro, Valentina Notarstefano and Simona Delle Monache
Cells 2025, 14(20), 1603; https://doi.org/10.3390/cells14201603 - 15 Oct 2025
Abstract
Two-dimensional cell cultures are crucial research tools, and they have been widely used, although they are not completely representative of biological processes in vivo due to the lack of tissue architecture and complexity. Recent advances in organoid technology have addressed these limitations and [...] Read more.
Two-dimensional cell cultures are crucial research tools, and they have been widely used, although they are not completely representative of biological processes in vivo due to the lack of tissue architecture and complexity. Recent advances in organoid technology have addressed these limitations and are revolutionizing the tools available for in vitro culture. Although there are no unified protocols for generating organoids, they can be obtained with various techniques, leading to cell aggregation by promoting cell adhesion. This work aims to generate and characterise organoid models of dental pulp from dental pulp stem cells (DPSCs), a type of mesenchymal stem/stromal cells known for their high regenerative potential and ease of accessibility, to establish a model for translational studies. The organoids were subjected to osteogenic differentiation conditions. Cell viability was evaluated using a CCK-8 assay, while osteogenic morphology and mineralization were confirmed by Alizarin red analysis, Raman microspectroscopy, and by immunofluorescence for the lineage markers expression. The Alizarin red analysis indicated a higher presence of calcium phosphate deposits in the differentiated organoids than in the control group (CTR). These results were confirmed by spectral profiles obtained using Raman microspectroscopy, which were attributable to a hydroxyapatite-based biomaterial. Immunofluorescence analysis also revealed increased expression of odonto/osteogenic markers (RUNX and OSX), alongside reduced expression of stemness markers. In conclusion, the organoids appeared to have successfully differentiated into an osteogenic lineage, forming a mineralized matrix containing hydroxyapatite and showing increased expression of relevant lineage markers. Full article
(This article belongs to the Special Issue 3D Cultures and Organ-on-a-Chip in Cell and Tissue Cultures)
23 pages, 10345 KB  
Article
A Patient-Derived Scaffold-Based 3D Culture Platform for Head and Neck Cancer: Preserving Tumor Heterogeneity for Personalized Drug Testing
by Alinda Anameriç, Emilia Reszczyńska, Tomasz Stankiewicz, Adrian Andrzejczak, Andrzej Stepulak and Matthias Nees
Cells 2025, 14(19), 1543; https://doi.org/10.3390/cells14191543 - 2 Oct 2025
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Abstract
Head and neck cancer (HNC) is highly heterogeneous and difficult to treat, underscoring the need for rapid, patient-specific models. Standard three-dimensional (3D) cultures often lose stromal partners that influence therapy response. We developed a patient-derived system maintaining tumor cells, cancer-associated fibroblasts (CAFs), and [...] Read more.
Head and neck cancer (HNC) is highly heterogeneous and difficult to treat, underscoring the need for rapid, patient-specific models. Standard three-dimensional (3D) cultures often lose stromal partners that influence therapy response. We developed a patient-derived system maintaining tumor cells, cancer-associated fibroblasts (CAFs), and cells undergoing partial epithelial–mesenchymal transition (pEMT) for drug sensitivity testing. Biopsies from four HNC patients were enzymatically dissociated. CAFs were directly cultured, and their conditioned medium (CAF-CM) was collected. Cryopreserved primary tumor cell suspensions were later revived, screened in five different growth media under 2D conditions, and the most heterogeneous cultures were re-embedded in 3D hydrogels with varied gel mixtures, media, and seeding geometries. Tumoroid morphology was quantified using a perimeter-based complexity index. Viability after treatment with cisplatin or Notch modulators (RIN-1, recombination signal-binding protein for immunoglobulin κ J region (RBPJ) inhibitor; FLI-06, inhibitor) was assessed by live imaging and the water-soluble tetrazolium-8 (WST-8) assay. Endothelial Cell Growth Medium 2 (ECM-2) medium alone produced compact CAF-free spheroids, whereas ECM-2 supplemented with CAF-CM generated invasive aggregates that deposited endogenous matrix. Matrigel with this medium and single-point seeding gave the highest complexity scores. Two of the three patient tumoroids were cisplatin-sensitive, and all showed significant growth inhibition with the FLI-06 Notch inhibitor, while the RBPJ inhibitor RIN-1 induced minimal change. The optimized scaffold retains tumor–stroma crosstalk and provides patient-specific drug response data within days after operation, supporting personalized treatment selection in HNC. Full article
(This article belongs to the Special Issue 3D Cultures and Organ-on-a-Chip in Cell and Tissue Cultures)
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Review

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35 pages, 2316 KB  
Review
Modeling Tumor Microenvironment Complexity In Vitro: Spheroids as Physiologically Relevant Tumor Models and Strategies for Their Analysis
by Shrey Shah and Gerard G. M. D’Souza
Cells 2025, 14(10), 732; https://doi.org/10.3390/cells14100732 - 17 May 2025
Cited by 4 | Viewed by 2977
Abstract
Drug delivery to solid tumors is challenged by multiple physiological barriers arising from the tumor microenvironment, including dense extracellular matrix, cellular heterogeneity, hypoxic gradients, and elevated interstitial fluid pressure. These features hinder the uniform distribution and accumulation of therapeutics, reducing treatment efficacy. Despite [...] Read more.
Drug delivery to solid tumors is challenged by multiple physiological barriers arising from the tumor microenvironment, including dense extracellular matrix, cellular heterogeneity, hypoxic gradients, and elevated interstitial fluid pressure. These features hinder the uniform distribution and accumulation of therapeutics, reducing treatment efficacy. Despite their widespread use, conventional two-dimensional monolayer cultures fail to reproduce these complexities, contributing to the poor translational predictability of many preclinical candidates. Three-dimensional multicellular tumor spheroids have emerged as more representative in vitro models that capture essential features of tumor architecture, stromal interactions, and microenvironmental resistance mechanisms. Spheroids exhibit spatially organized regions of proliferation, quiescence, and hypoxia, and can incorporate non-tumor cells to mimic tumor–stroma crosstalk. Advances in spheroid analysis now enable detailed evaluation of drug penetration, cellular migration, cytotoxic response, and molecular gradients using techniques such as optical and confocal imaging, large-particle flow cytometry, biochemical viability assays, and microfluidic integration. By combining physiological relevance with analytical accessibility, spheroid models support mechanistic studies of drug transport and efficacy under tumor-like conditions. Their adoption into routine preclinical workflows has the potential to improve translational accuracy while reducing reliance on animal models. Full article
(This article belongs to the Special Issue 3D Cultures and Organ-on-a-Chip in Cell and Tissue Cultures)
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Other

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53 pages, 2035 KB  
Systematic Review
Brain Organoid Transplantation: A Comprehensive Guide to the Latest Advances and Practical Applications—A Systematic Review
by Yu-Ping Shen and Zaal Kokaia
Cells 2025, 14(14), 1074; https://doi.org/10.3390/cells14141074 - 14 Jul 2025
Viewed by 4063
Abstract
Brain organoid technology has seen significant development in recent years. This self-organized, three-dimensional, organ-oriented brain tissue model can recapitulate the process of neurogenesis and consists of diverse cell types and cellular architecture. Transplanting brain organoids in vivo could be a potential tool from [...] Read more.
Brain organoid technology has seen significant development in recent years. This self-organized, three-dimensional, organ-oriented brain tissue model can recapitulate the process of neurogenesis and consists of diverse cell types and cellular architecture. Transplanting brain organoids in vivo could be a potential tool from bench to clinical research and has been studied for many purposes. To investigate and summarize the methodology, findings, and applications of this novel technique from current evidence, we conducted this systematic review by searching PubMed and the Embase databases for the literature ranging from 2013 to 2024. A total of 480 articles were identified, and 24 of them met the inclusion criteria. The results revealed that brain organoid transplantation had promising graft survival, neural proliferation, differentiation, and maturation, axonal growth, and functional integration into the host neuronal circuit, and has been applied to multiple applications, such as therapeutic usage, cell study platforms, and disease modeling. However, heterogeneity among studies, some significant challenges, and ethical issues remain to be considered. This comprehensive review will provide an update of what is known about this powerful, innovative method and discuss some practical aspects for future research. Full article
(This article belongs to the Special Issue 3D Cultures and Organ-on-a-Chip in Cell and Tissue Cultures)
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