Advances in Three-Dimensional Culture Systems: Bridging Biology and Medicine

A special issue of Bioengineering (ISSN 2306-5354). This special issue belongs to the section "Biomedical Engineering and Biomaterials".

Deadline for manuscript submissions: 30 November 2025 | Viewed by 908

Special Issue Editor


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Guest Editor
Department of Engineering Technology, College of Technology, University of Houston, Houston, TX 77004, USA
Interests: 3D culture systems; biomaterials; tissue engineering; microscope image processing; multidimensional image analysis; 3D image processing and analysis; cytometry

Special Issue Information

Dear Colleagues,

Three-dimensional (3D) culture systems have emerged as powerful tools in biology and medicine, enabling researchers to recapitulate the complexity of in vivo environments in vitro. This Special Issue delves into the latest developments in 3D culture technologies, their applications across various biological and medical disciplines, and the implications for understanding disease mechanisms and therapeutic interventions.

The Special Issue on three-dimensional culture systems in biology and medicine aims to provide a comprehensive overview of the latest advancements and applications in the field. By bridging disciplines and fostering collaboration between engineers, biologists, and clinicians, this collection aims to accelerate the translation of 3D culture technologies into impactful biomedical solutions, ultimately improving our understanding of disease pathogenesis and enhancing patient care. Both original research contributions and review papers are welcome, which may include, but are not limited to, the following topics:

Reviewing state-of-the-art techniques for engineering 3D matrices, scaffolds, and organoids to mimic native tissue architecture and cell–cell interactions. Reviews can focus on advances in biofabrication methods, including 3D bioprinting and microfluidic-based approaches, for creating precise and customizable 3D culture platforms and strategies to incorporate biochemical and biophysical cues into 3D culture systems to better mimic the physiological microenvironment.

Modeling disease and physiological processes: presenting case studies demonstrating the utility of 3D culture systems in modeling various diseases, such as cancer, neurodegenerative disorders, and infectious diseases.

Translation to clinical applications: discussing regulatory considerations and quality control standards for the clinical translation of 3D culture-based therapies and diagnostic tools. Highlighting ongoing clinical trials and emerging therapeutic strategies based on insights gained from 3D culture studies.

Prof. Dr. Fatima A. Merchant
Guest Editor

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Keywords

  • 3D culture platforms
  • microengineered 3D systems
  • biomaterials for 3D culture
  • engineering complex 3D microenvironments
  • 3D systems for modeling disease and physiological processes
  • 3D culture-based therapies and diagnostic tools
  • translation of 3D systems for clinical applications

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Published Papers (1 paper)

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Research

22 pages, 4011 KB  
Article
Extracellular Vesicle Secretion from 3D Culture of Human Adipose-Derived Mesenchymal Stem Cells in Scalable Bioreactors
by Shaoyang Ma, Justice Ene, Colton McGarraugh, Shaoxuan Ma, Colin Esmonde, Yuan Liu and Yan Li
Bioengineering 2025, 12(9), 933; https://doi.org/10.3390/bioengineering12090933 - 29 Aug 2025
Viewed by 238
Abstract
Human mesenchymal stem cells (hMSCs) and their secreted extracellular vesicles (EVs) are promising therapeutics to treat degenerative or inflammatory diseases such as ischemic stroke and Alzheimer’s disease (AD). hMSC-EVs have the coveted ability to contain therapeutically relevant biomaterials; however, EV biogenesis is sensitive [...] Read more.
Human mesenchymal stem cells (hMSCs) and their secreted extracellular vesicles (EVs) are promising therapeutics to treat degenerative or inflammatory diseases such as ischemic stroke and Alzheimer’s disease (AD). hMSC-EVs have the coveted ability to contain therapeutically relevant biomaterials; however, EV biogenesis is sensitive to the culture microenvironment in vitro. Recently, the demand for hMSC-EVs has increased dramatically, highlighting the need for scalable bioreactors for large-scale biomanufacturing. In this study, adipose-derived hMSCs were seeded in 2D plates, an ultralow-attachment (ULA) plates as static aggregates, a novel vertical wheel bioreactor (VWBR) as aggregates, and a spinner flask bioreactor (SFB). EV secretion was quantified and compared using ExtraPEG-based ultracentrifugation and nanoparticle tracking analysis. Compared to the 2D group, significantly higher total EV production and cell productivity in the bioreactors were observed, as well as the upregulation of EV biogenesis genes. Furthermore, there was increased EV production in the VWBR compared to the SFB and the static ULA control. Functional assessments demonstrated that EVs, when delivered via culture medium or hydrogel-based systems, significantly attenuated oxidative stress elevation, suppressed proinflammatory cytokine secretion (e.g., TNF-α) and gene expression, and inhibited nuclear factor kappa-light-chain-enhancer of activated B-cell (NF-κB) activation and neurodegenerative markers across in vitro assays. These findings suggest EV-mediated mitigation of oxidative and inflammatory pathways, potentially through modulation of the NF-κB signaling cascade. This study shows the influence of bioreactor types and their microenvironments on EV secretion in hMSCs and their applications in hMSC-EV production and bioengineering. Full article
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