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Molecular Biology of 3D Cell and Tissue Culture Systems: Benefits to Research and Disease Diagnostics

Special Issue Editor

Special Issue Information

Dear Colleagues,

Three-dimensional (3D) biology dates back over 110 years to the pioneering work of the French surgeon and researcher Alexis Carrel, who won the Nobel Prize in Physiology in 1912. His work encompassed unique and innovative applications in tissue and cell culturing, with his focus directed toward anastomosis and revolutionary suturing techniques. To date, this field has rapidly metamorphosized, encompassing a wide variety of applications.

This Special Issue will welcome manuscripts that explore the many evolving benefits of 3D physiological systems biology as compared to standard 2D culture systems in research and preclinical arenas. These include, but are not limited to, microgravity-related applications, cellular and molecular outcomes (omics), cellular and tissue toxicity, drug discovery applications, 3D tissues as viral research and discovery targets, and 3D tissue engineering in the context of potential transplantation, regenerative medicine (stem cells and regeneration), and bioprinting applications. In the arena of “omics”, we invite the submission of manuscripts which address, but are not limited to, genomics, proteomics, metabolomics, transcriptomics, and the spatial biology of 3D physiological systems. Manuscripts addressing the challenges of developing authentic tissue “mimics” with regard to functional accuracy and structural recapitulation will also be considered favourably.

Dr. Thomas J. Goodwin
Guest Editor

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Keywords

  • 3D physiological relevance vs. 2D biology, 3D research, and diagnostic systems
  • evolving 3D “omics” applications
  • research and clinical medicine
  • drug applications
  • toxicity evaluations
  • “Omics” 
  • spatial biology of 3D

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Published Papers (1 paper)

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Research

21 pages, 13574 KB  
Article
Identification of microRNA-Related Target Genes for the Development of Otic Organoids
by Sehee Lee, Sungjin Park, Euyhyun Park, Gi Jung Im and Jiwon Chang
Int. J. Mol. Sci. 2025, 26(21), 10627; https://doi.org/10.3390/ijms262110627 - 31 Oct 2025
Viewed by 414
Abstract
Mammalian hearing loss is typically permanent due to the inability to replace damaged cochlear hair cells. However, the neonatal mice inner ear demonstrates regenerative capacity, with cochlear floor cells proliferating and differentiating into organoids containing new hair cells and supporting cells, yet the [...] Read more.
Mammalian hearing loss is typically permanent due to the inability to replace damaged cochlear hair cells. However, the neonatal mice inner ear demonstrates regenerative capacity, with cochlear floor cells proliferating and differentiating into organoids containing new hair cells and supporting cells, yet the governing molecular mechanisms remain poorly understood. Here, we isolated extracellular vesicles (EVs) from inner ear organoids at proliferation and differentiation stages, characterized their EV miRNA profiles through sequencing, and validated findings using public transcriptomic datasets to elucidate miRNA-mediated regulatory mechanisms during inner ear development. Inner ear organoids were successfully developed from cochlear duct cells, expressing otic progenitor marker SOX2 and hair cell marker Myo7A and demonstrating functional mechano-transduction activity through FM1-43 uptake. Small RNA sequencing identified 35 differentially expressed EV miRNAs between developmental stages. Integrated analysis with public transcriptome datasets revealed 18 genes with significant differential expression, leading to identification of three key regulatory genes—Trp53, Ezh2, and Zbtb4—that exhibited dynamic spatiotemporal expression during inner ear maturation. Pathway analysis demonstrated that these genes are associated with DNA Repair, P53, and Wnt/β-Catenin signaling with remarkable cell-type specificity. Our results demonstrate that EV miRNAs are temporally regulated during organoid development, with predominant downregulation during differentiation. These findings provide crucial insights into developmental mechanisms that could optimize organoid-based models and guide EV miRNA-based therapeutic strategies for hearing restoration. Full article
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