Balys, M. | bioRxiv Science

bioRxiv2024

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↗

bioRxiv2020

Comparative analysis of single-cell RNA Sequencing Platforms and Methods

Single-cell RNA sequencing (scRNA-seq) offers great new opportunities for increasing our understanding of complex biological processes. In particular, development of an accurate Human Cell Atlas is largely dependent on the rapidly advancing technologies and molecular chemistries employed in scRNA-seq. These advances have already allowed an increase in throughput for scRNA-seq from 96 to 80,000 cells on a single instrument run by capturing cells within nano-liter droplets. While this increase in throughput is critical for many experimental questions, a thorough comparison between microfluidic-, plate-, and droplet-based technologies or between multiple available platforms utilizing these technologies is largely lacking. Here, we report scRNA-seq data from SUM149PT cells treated with the histone deacetylase inhibitor TSA vs. untreated controls across several scRNA-seq platforms (Fluidigm C1, WaferGen iCell8, 10X Genomics Chromium Controller, and Illumina/BioRad ddSEQ). The primary goal of this project was to demonstrate RNA sequencing (RNA-seq) methods for profiling the ultra-low amounts of RNA present in individual cells, and this report discusses the results of the study as well as technical challenges/lesson learned and present general guidelines for best practices in sample preparation and analysis.

genomics↗