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Organoids

Organoids is an international, peer-reviewed, open access journal on all aspects of organoids published quarterly online by MDPI.

All Articles (87)

Hepatoblastoma (HB) is a paediatric liver malignancy arising from hepatic precursor cells, with >90% of cases harbouring a mutation in exon 3 of CTNNB1. We present a fully genetically characterised HB tumour organoid (tumoroid) biobank, which allows for in vitro studies of disease progression and clonal dynamics in vitro. We established a biobank of 14 tumoroid lines from 9 different patients. Tumours and tumoroids were characterised by whole genome sequencing (WGS) and histology, revealing strong concordance in cell morphology and β-catenin staining. In tumour—tumoroid pairs, identical pathogenic CTNNB1 variants were found, alongside shared copy number alterations (CNAs) and mutations. Variant allele frequency (VAF) was consistently higher in tumoroids, indicating increased tumour purity in vitro. In addition to CTNNB1, we frequently observed ARID1A alterations (single-nucleotide variants [SNVs] or CNAs in 56% of patients), and MYC gains as described previously. In paired pre- and post-treatment samples, we observed a clear increase in mutational load, attributed to a chemotherapy signature. Notably, from one patient, we analysed 4 tumour samples (3 post-treatment) with 4 matching tumoroid lines, all carrying a novel BCL6 mutation and loss of ARID1A. Mutational profiles varied across samples from different locations, suggesting intratumoral heterogeneity and clonal selection during tumoroid derivation. Taken together, this biobank allows detailed analysis of HB tumour biology, including treatment-induced progression and clonal dynamics across temporally and spatially distinct samples.

18 January 2026

(A) schematic overview of biobanking process. (B). Sample overview with patient identifier and metadata (age, sex, and time of procurement). P indicates primary sample usually at time of diagnosis, R indicates samples from resection or recurrence. Tumour samples are marked T, and tumoroid samples are marked O. Sex is shown by M(ale) or F(emale), and age in years. WGS data is shown in green. (C). Graph showing the time in culture and number of passages for each tumoroid line. (D). Representative brightfield images of hepatoblastoma tumoroid cultures. (E). H&E stain (left) and β-catenin stain (right) of tumour tissue (top panels) and tumoroid lines (bottom panels).

Human umbilical cord-derived mesenchymal stem cells (hUC-MSCs) possess the potential for chondrogenic differentiation, offering a promising alternative source for cartilage regeneration. To address the limited availability and expansion capacity of autologous chondrocytes, we investigated the effect of co-overexpression of Sox9, TGFβ1, and type II collagen (Col II) on the chondrogenic differentiation of hUC-MSCs using both 2D and 3D pellet culture systems. Following transfection, the cells exhibited a chondrocyte-like morphology and a marked downregulation of the stemness marker Stro-1. After 21 days in a 3D pellet culture system, the cells formed cartilage-like tissue characterized by the strong expression of chondrocyte-specific genes (Sox9, TGFβ1, Col II, Aggrecan) along with the significant secretion of sulfated glycosaminoglycans (sGaGs). These effects were attributed to enhanced cell–cell contact and extracellular matrix interactions promoted by the 3D environment. Our findings suggest that genetically modified hUC-MSCs cultured in a 3D pellet system represent a robust in vitro model for cartilage regeneration, with potential applications in transplantation and drug toxicity screening.

14 January 2026

Characterization of human umbilical cord-derived mesenchymal stem cells. (A) Representative images of the homogeneous population of cells showing spindle-like morphology from P1 to P6. (B) Isolated cells positively expressed MSC-specific markers, including CD105, vimentin, CD117, CD29, Lin28, and Stro1. CD45 and HLA-DR, as hematopoietic and immunity markers, were not expressed. Alexa Fluor 488 and DAPI were used to stain the cytoskeleton and nuclei of cells, respectively. (C) Illustration of the phenotypic assessment of hUC-MSCs positive for vimentin, CD90, and CD105 and negative for CD45. (D) Tri-lineage differentiation assay shows successful production of calcium deposits, proteoglycans, and oil droplets by osteocytes, chondrocytes, and adipocytes, respectively. Images were captured using a microscope at 10× magnification.

Decellularized Extracellular Matrix for Organoids Development and 3D Bioprinting

  • Elena Gkantzou,
  • Alexandro Rodríguez-Rojas and
  • Iwan A. Burgener
  • + 4 authors

Organoids are three-dimensional multicellular structures that mimic key aspects of native tissues consisting ideal tools to study organ development and pathophysiology when incorporated in customized bioscaffolds. In vivo, the extracellular matrix (ECM) maintains tissue integrity and regulates cell adhesion, migration, differentiation, and survival through biochemical and mechanical signals. Tissue-derived decellularized extracellular matrix (dECM) can preserve organ-specific biochemical signals and cell-adhesive motifs, creating a bioactive environment that supports physiologically relevant organoid growth. 3D bioprinting technology marks a transformative phase in organoid research by enhancing the structural and functional complexity of organoid models and expanding their application in pharmacology and regenerative medicine. These systems enhance tissue modeling and drug testing while adhering to the principles of animal replacement, reduction, and refining (3Rs) in research. Remaining challenges include donor variability, limited mechanical stability, and the lack of standardized decellularization protocols that can be addressed by adopting quality and safety metrics. The combination of dECM-based biomaterials and 3D bioprinting holds great potential for the development of human-relevant, customizable, and ethically sound in vitro models for regenerative medicine and personalized therapies. In this review, we discuss the latest (2021–2025) developments in applying extracellular matrix bioprinting techniques to organoid technology, presenting examples for the most commonly referenced organoid types.

8 January 2026

The main steps and processes for the transformation of extracellular matrix into a bioink for 3D bioprinting applications. Three main phases (in blue) that contain several steps (in orange) are followed to reach from dECM bioink formulation to a 3D-printed biological model. Steps 1–4 are essential, while the specific steps during the 3D bioprinting phase (6–8) may vary depending on the characteristics of the final material and its intended application. Part of the figure was created with BioRender.

Organoids consisting of primary human cells, i.e., astrocytes, pericytes, and endothelial cells, form a functional blood–brain barrier (BBB) in vitro. The ability of FITC-dextran (70 kDa), calcium phosphate nanoparticles (100 nm), Escherichia coli bacteria (2 µm), and MS2 coliphages (27 nm, a model for viruses) to penetrate the BBB under normoxic and hypoxic conditions (2.5% oxygen) for up to 12 days was assessed by fluorescence microscopy and confocal laser scanning microscopy. All agents were fluorescently labeled to trace them inside the organoids. Under normoxia, FITC-dextran, calcium phosphate nanoparticles, E. coli bacteria and MS2 coliphages did not penetrate the BBB. However, oxygen deficiency (hypoxia) triggered the penetration of the BBB by FITC-dextran and E. coli cells. This was underscored by a strong hypoxic center inside the organoids that developed in the presence of E. coli bacteria.

2 January 2026

Schematic representation of the culture process of BBB organoids under normoxic and hypoxic conditions (image created with BioRender).

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Organoids - ISSN 2674-1172