From the Journals

Researchers present cellular atlas of the human gut

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The final answer on the human intestinal epithelium

Single cell transcriptomics has revolutionized our understanding of complex tissues, as this technology enables the identification of rare and/or novel cell types. Gastrointestinal science has benefited greatly from these technical advances, with multiple studies profiling liver, pancreas, stomach and intestine in health and disease, both in mouse and human samples.

Klaus H. Kaestner, PhD, MS, is with the department of genetics and the Center for Molecular Studies in Digestive and Liver Diseases at the University of Pennsylvania, Philadelphia

Dr. Klaus H. Kaestner

The study by Burclaff and colleagues recently published in Cellular and Molecular Gastroenterology and Hepatology is the most complete analysis of the healthy human intestine to date, profiling over 12,000 single epithelial cells from three donors along the anterior-posterior axis from duodenum to descending colon. In a truly monumental work covering 35 journal pages, the authors not only delineate in great detail the various cell lineages – from stem cell to full differentiated enterocyte, for instance – but also make surprising discoveries that will change our thinking about fundamental issues in gastrointestinal biology. For instance, they find that human small intestinal Paneth cells, known for the production of antimicrobial peptides and long thought to be a critical component of the intestinal stem cell niche, do not express any of the niche factors, including mitogens such as epidermal growth factor, that had been attributed to Paneth cells in mice. The authors conclude that human Paneth cells are not major niche-supporting cells, in keeping with the recent identification of subepithelial telocytes as the critical cells that support crypt proliferation in mice. In addition, the authors’ analysis of so called “BEST4” cells, an intestinal lineage absent from the mouse gut, suggests a novel function for this rare cell type in metal absorption.

In sum, this study is the “final answer” for GI biologists needing a complete compendium of all genes active in the multitude of specialized human intestinal epithelial cells.

Klaus H. Kaestner, PhD, MS, is with the department of genetics and the Center for Molecular Studies in Digestive and Liver Diseases at the University of Pennsylvania, Philadelphia. He declares having no conflicts of interest.



New research sheds light on how different cell types behave across all intestinal regions and demonstrates variations in gene expression between these cells across three independent organ donors.

Research led by Joseph Burclaff, PhD, of the University of North Carolina at Chapel Hill, explained that the regional differences observed in the study “highlight the importance of regional selection when studying the gut.” Dr. Burclaff and colleagues, whose findings were published online in Cellular and Molecular Gastroenterology and Hepatology, wrote that they hope their “database serves as a resource to understand how drugs affect the intestinal epithelium and as guidance for future precision medicine approaches.”

In the study, Dr. Burclaff and colleagues performed single-cell transcriptomics that covered the duodenum, jejunum, ileum, as well as ascending, descending, and transverse colon from three independently processed organ donors. The donors varied in age, race, and body mass index.

The investigators evaluated 12,590 single epithelial cells for organ-specific lineage biomarkers, differentially regulated genes, receptors, and drug targets. The focus of the analyses was on intrinsic cell properties and their capacity for response to extrinsic signals found along the gut axis.

The research group assigned cells to 25 epithelial lineage clusters. According to the researchers, multiple accepted intestinal cell markers did not specifically mark all intestinal stem cells. In addition, the investigators explained that lysozyme expression was not unique to Paneth cells, and these cells lacked expression of certain “expected niche factors.” In fact, the researchers demonstrated lysozyme’s insufficiency for marking human Paneth cells.

Bestrophin-4þ (BEST4þ) cells, which expressed neuropeptide Y, demonstrated maturational differences between the colon and small intestine, suggesting organ-specific maturation for tuft and BEST4+ cells. In addition, the data from Dr. Burclaff and colleagues suggest BEST4+ cells are engaged in “diverse roles within the intestinal epithelium, laying the groundwork for functional studies.”

The researchers noted that “tuft cells possess a broad ability to interact with the innate and adaptive immune systems through previously unreported receptors.” Specifically, the researchers found these cells exhibit genes believed to be important for taste signaling, monitoring intestinal content, and signaling the immune system.

Certain classes of cell junctions, hormones, mucins, and nutrient absorption genes demonstrated “unappreciated regional expression differences across lineages,” the researchers wrote. The investigators added that the differential expression of receptors as well as drug targets across lineages demonstrated “biological variation and the potential for variegated responses.”

The researchers noted that while the regional differences identified in their study show the importance of regional selection during gut investigations, several previous colonic single-cell RNA sequencing studies did not specify the sample region or explain “if pooled samples are from consistent regions.”

In the study, the investigators also assessed how drugs may affect the intestinal epithelium and why certain side effects associated with pharmacologic agents occur. The researchers identified 498 drugs approved by the Food and Drug Administration that had 232 primary gene targets expressed in the gut epithelial dataset.

In their analysis, the researchers found that carboxylesterase-2, which metabolizes the drug irinotecan into biologically active SN-38, is the highest expressed phase 1 metabolism gene in the small intestine. Phase 2 enzyme UGT1A1, which inactivates SN-38, features low gut epithelial expression. The researchers explained that this finding suggests the cancer drug irinotecan may feature prolonged gut activation, supporting the notion that the orally administered agent may have efficacy against cancers of the intestine.

The researchers concluded their “database provides a foundation for understanding individual contributions of diverse epithelial cells across the length of the human intestine and colon to maintain physiologic function.”

The researchers reported no conflicts of interest with the pharmaceutical industry. The study received no industry funding.

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