Molecular and Functional Characterization of Human Intestinal Organoids and Monolayers for Modeling Epithelial Barrier
Patient-derived organoid models can transform drug discovery for inflammatory bowel disease, but differentiation and functional characterization inconsistencies limit that transformation. Jelinsky et al. profiled molecular and cellular features across a range of intestinal organoid models using bulk RNA sequencing, among other technologies, and examined differentiation and establishing a functional epithelial barrier.
- DOI: 10.1093/ibd/izac212
- PMID: 36356046
- Services: Bulk RNA sequencing
- Species: Human
- Sample type: Intestine, Organoids
BMP gradient along the intestinal villus axis controls zonated enterocyte and goblet cell states
Beumer et al. show that the bone morphogenetic protein (BMP) signaling pathway controls the creation of functional zones along the crypt-villus axis. A gene lipid uptake gene signature is enriched in the villus tip and could be therapeutically exploited with BMP inhibitors.
- DOI: 10.1016/j.celrep.2022.110438
- PMID: 35235783
CD127+ CD94+ innate lymphoid cells expressing granulysin and perforin are expanded in patients with Crohn’s disease
The researchers designate two distinct innate lymphoid cell subtypes. Then, using single-cell RNA sequencing and further characterization methods, one subtype was found to express toxic compounds granulysin and perforin in the intestines of Chron’s disease patients.
- DOI: 10.1038/s41467-021-26187-x
- PMID: 34615883
Collection of cells for single-cell RNA sequencing using high-resolution fluorescence microscopy
Segeren et al. describe a workflow to capture, image, and collect fluorescent human retina pigment epithelium cells for SORT-seq using the VYCAP puncher system. This protocol is relevant for cells that cannot be FACS-sorted.
- DOI: 10.1016/j.xpro.2021.100718
- PMID: 34401784
SARS-CoV-2 productively infects human gut enterocytes
How can you explain gastrointestinal symptoms after SARS-CoV-2 infection? Lamers et al. demonstrated SARS-CoV-2 replicates in the enterocytes of human intestinal organoids. Bulk mRNA sequencing showed RNA expression changes in infected organoids.
- DOI: 10.1126/science.abc1669
- PMID: 32358202
- Services: Bulk RNA sequencing
- Species: Human
- Sample type: Intestine, Lung
High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells
Beumer et al. describe an organoid-based platform for functional studies of human enteroendocrine cells, the intestines’ hormone-excreting cells. They made a single-cell mRNA atlas for different subtypes and identified the secreted products.
- DOI: 10.1016/j.cell.2020.04.036
- PMID: 32407674
- Services: Bulk RNA sequencing, SORT-seq
- Species: Human
- Sample type: Intestine
Identification of Enteroendocrine Regulators by Real-Time Single-Cell Differentiation Mapping
This paper presents Neurog3Chrono, a bi-fluorescent reporter for the differentiation process of enteroendocrine cells, the intestines’ hormone-excreting cells. It measures fluorescence in time and per cell, enabling the real-time arrangement of single-cell gene expression profiles.
- DOI: 10.1016/j.cell.2018.12.029
- PMID: 30712869
- Services: Bulk RNA sequencing, SORT-seq
- Species: Mouse
- Sample type: Intestine, Stem cells