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Biology subjects

Benedetti, G.

Publications and source records attributed to Benedetti, G..

3 recordsLinked to original sources

WS6 enables scalable ex vivo expansion and gene editing of epithelial basal stem cells

Modeling human epithelial diseases and developing cell-based therapies require robust methods to expand and manipulate epithelial stem and progenitor cells in vitro. Basal stem/progenitor cells from stratified epithelia can be expanded in 3T3-J2 fibroblast feeder cell co-culture systems, and the addition of the ROCK inhibitor Y-27632 enhances proliferation and culture longevity, a phenomenon described as conditional reprogramming. Here, we present a method incorporating the small molecule WS6 to further improve the proliferation and lifespan of cultured epithelial cells from multiple tissues, including airway, skin, and thymus. Cells maintained in this medium ( EpMED; FAD+Y+WS6) retain basal stem/progenitor cell identity and function, including the capacity to differentiate. We demonstrate their capacity to engraft in vivo in a tracheal transplantation model. In a second application, we generate clonal CRISPR-Cas9 genome edited nasal cultures, introducing targeted knockouts of DNAH5 or DNAI2 to create primary ciliary dyskinesia disease models. We anticipate that our method will have broad applications in epithelial cell biology, disease modeling, and regenerative medicine, while reducing reliance on immortalized or cancer cell lines and animal experimentation.

cell biology↗

Human Gastric Multi-Regional Assembloids Favour Functional Parietal Maturation and Allow Modelling of Antral Foveolar Hyperplasia

Patient-derived human organoids have the remarkable capacity to self-organise into more complex structures. However, to what extent gastric organoids can recapitulate human stomach physiological functions remain unexplored. Here, we report how region-specific gastric organoids can self-assemble into complex multi-regional assembloids showing functional response to drugs targeting the ATPase H+/K+ pump. The assembloids show preserved fundus, body, and antrum regional identity, and gastric-specific crosstalk pathways arise. The increased complexity and cross-communication between the different gastric regions, allow for the emergence of the elusive parietal cell type, responsible for the production of gastric acid, with functional response to drugs targeting the ATPase H+/K+ pump. Remarkably, we generated assembloids from PMM2-HIPKD-IBD paediatric patients (Phosphomannomutase 2 - Hyperinsulinemic hypoglycaemia and autosomal recessive polycystic kidney disease - Inflammatory bowel disease), a genetic condition found to be associated with unusual antral foveolar hyperplasia and hyperplastic polyposis. The cellular mechanisms behind such phenomena are poorly understood, and an exhaustive experimental model is needed. The {Delta}PMM2 multi-regional assembloid we have generated efficiently recapitulates hyperplastic-like antral regions, with decreased mucin secretion and glycosylated ATP4b, which results in impaired gastric acid secretion. Multi-regional gastric assembloids, generated using adult-stem cell-derived organoids, successfully recapitulate the structural and functional characteristics of the human stomach, offering a promising tool for studying gastric epithelial interactions and disease mechanisms previously challenging to investigate in primary models.

cell biology↗

RNA Secondary Structure Prediction Using a Genetic Algorithm with a Selection Method Based on Free Energy Value and Topological Index

This paper presents a genetic algorithm designed to predict RNA secondary structures, which utilizes selection criteria based on free energy (fitness) and topological similarity. This approach represents structural information using a simple number, facilitating comparisons between foldings. The simplified graph representation identifies similarities between structures that have the same type of branches. The results demonstrate that the algorithm identifies the final secondary structure with the same level of precision as the commonly used dynamic programming, but with the advantage of producing more optimal structures with different topologies. This approach maintains high population diversity and allows for the exploration of many suboptimal structures in parallel, avoiding the possibility of getting stuck in a local minimum. This permits the investigation of not only the structure with the minimum free energy, but also of other low-energy structures with different topologies that are closer to the natural fold.

bioinformatics↗