Project title

Using mini stomach models to study rare childhood gastric diseases 

Supervisors


Background

Gastric epithelial diseases in children, while rare, can present with severe and complex clinical manifestations that are often poorly understood. Two such conditions include PMM2-related Antral Foveolar Hyperplasia (AFH), associated with the rare PMM2-HIPKD-IBD syndrome (Kiparissi et al.,2023), and Collagenous Gastritis (CG) (Kamimura et al.,2015), a rare inflammatory condition with excessive collagen deposition and epithelial damage. Traditional organoids and animal models fail to replicate the regional architecture and functional diversity of the human stomach. Recent advances in gastric assembloid technologies offer the potential to model region-specific physiology and disease phenotypes in vitro (Benedetti et al., 2023). Our group has recently developed a multi-regional gastric assembloids (MRAs) that recapitulate the antrum-body-fundus structure and function, including acid secretion and mucin production (Jones et al.,2024). These models are uniquely positioned to unravel disease mechanisms in rare gastric disorders. However, diseases like CG also involve the stromal compartment, prompting the need to develop epithelium-mesenchyme assembloid systems.

Aims

This PhD project will develop and apply human gastric assembloid systems to model rare paediatric gastric diseases. The specific aims are:

  1. To characterise epithelial differentiation and function in PMM2-deficient multi-regional assembloids derived from patient biopsies.
  2. To test genetic correction (CRISPR) and pharmacological rescue (repurposed drug) strategies in PMM2 assembloids.
  3. To develop and characterise novel epithelial–mesenchymal assembloids to model Collagenous Gastritis.
  4. To identify disease-specific cellular and molecular signatures using transcriptomic and functional assays.


Methods

  • Organoid culture: Gastric organoids from antrum, body, and fundus will be established from paediatric tissue samples.
  • Assembloid formation: Organoids will be embedded in ECM hydrogel (Giobbe et al.,2019) and self-assembled into MRAs. For CG, co-culture with primary mesenchymal cells will be optimised.
  • Genome editing: CRISPR base-editing will be used to correct PMM2 promoter variants in patient-derived assembloids.
  • Functional assays: Acid secretion (pH dye), mucin production (ELISA, lectin staining), and proliferation (Ki67 IF) will be quantified.
  • Molecular analysis: scRNA-seq, spatial transcriptomics, and immunostaining will profile regional cell types and disease-specific pathways.
  • Collagen quantification: CG assembloids will be assessed for collagen deposition using second harmonic generation imaging and Masson’s trichrome staining.


Timeline

Year 1 

  • Training in organoid culture, CRISPR editing, and imaging
  • Optimisation of gastric assembloid formation
  • Generation of PMM2 and CG patient-derived organoid lines

 

Year 2 

  • Genetic correction and drug treatment of PMM2 assembloids
  • Development of epithelium-mesenchyme CG assembloids
  • Functional and transcriptomic profiling

 

Year 3

  • Mechanistic analysis and therapeutic validation
  • Data integration and manuscript preparation
  • Presentation at national/international conferences

 

References

  1. Benedetti, G. … Giobbe GG. Generation of human gastric assembloids from primary fetal organoids. Pediatr Surg Int. 2023 Nov 24;40(1):6
  2. Giobbe, G.G. et al. Extracellular matrix hydrogel enables endodermal organoid culture. Nat Commun. 2019.
  3. Jones, B.C. … Giobbe, G.G. & De Coppi, P. Human Gastric Multi-Regional Assembloids… bioRxiv 2024.07.08.602480 (in press Nat. Biomed. Eng).
  4. Kamimura, K. et al. Collagenous gastritis:Review. World J Gastrointest Endosc 7, 265 (2015).
  5. Kiparissi, F. et al. PMM2 variants and antral foveolar hyperplasia. Hum Genet. 2023.


Who should students contact?

Giovanni Giobbe (g.giobbe@ucl.ac.uk)

Research topic

Paediatric surgery