The gastrointestinal tract (GI) is the pathway from your mouth to your esophagus, stomach, and small and large intestines. In the GI tract, nutrients and water from food are absorbed to help keep your body healthy. Using single-cell RNA sequencing, researchers from the Hubrecht Institute report they studied the cellular composition of the upper gastrointestinal tract and have identified and characterized rare cell types.

Their findings, “Human gastrointestinal epithelia of the esophagus, stomach, and duodenum resolved at single-cell resolution,” was published in Cell Reports and led by Hans Clever, PhD, principal investigator at the Hubrecht Institute for Developmental Biology and Stem Cell Research.

Their findings provide detailed gene expression analyses for all epithelial cells in these organs. The rare cell type that was identified is most likely responsible for the secretion of high volumes of water in humans. This cell type provides a link to gastrointestinal defects in patients with cystic fibrosis.

Single-cell RNA sequencing (scRNA-seq) gives researchers the ability to study the presence and quantity of RNA in individual cells. It can reveal complex and rare cell populations, uncover regulatory relationships between genes, and track the trajectories of distinct cell lineages in development

The researchers obtained biopsies from healthy human tissue and compared the obtained data to mouse datasets.

“The upper gastrointestinal tract, consisting of the esophagus, stomach, and duodenum, controls food transport, digestion, nutrient uptake, and hormone production,” noted the researchers. “By single-cell analysis of healthy epithelia of these human organs, we molecularly define their distinct cell types.”

Staining for KRT15 and COL17A1 in healthy human esophageal epithelium. [Georg Busslinger, PhD, copyright Hubrecht Institute]

The researchers first observed an esophageal stem cell population with high expression of the COL17A1 gene. Mutations in this gene are associated with the development of blistering disease in the skin, however defects with the esophagus are rarely reported in these patients.

The researchers characterized the cell composition in the stomach and found that the cells responsible for histamine production also express luteinizing hormone (LH), which plays a role in ovulation during the female reproductive cycle and for regulating testosterone levels in men. More research is needed to determine why the cells express the hormone in the stomach.

When studying the upper part of the small intestine, the researchers found a rare cell type with high expression of four genes, which are all linked to the secretion of high volumes of water. The most prominent member is the CFTR gene. Mutations in CFTR cause cystic fibrosis (CF).

The researchers noted that studying human and mouse datasets for the gastrointestinal organs revealed differences in gene expression patterns between humans and mice. The cells in the stomach producing LH were only seen in humans and the cell type secreting high volumes of water does not exist in mice. These findings suggest that an alternative method such as organoids may be better suited than the common mice studies used to study human disease.

“The results provide insight into the molecular characteristics of individual cell types and how they may function in the healthy epithelium. Moreover, these data serve as a resource for scientists everywhere,” concluded Georg Busslinger, PhD, first author of the paper and postdoctoral fellow at the Hans lab.