3d illustration human body crohn's intestines infection with clipping path.
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Scientists at the University of Cambridge and the Wellcome Sanger Institute have carried out single-cell sequencing of cells involved in the earliest stages of human gut development, to reveal intricate cellular mechanisms. Their results suggest that specific cell pathways that are active in the fetal gut epithelium are then reactivated in the gut tissue of children with Crohn’s disease (CD). The research, which was carried out as part of the global Human Cell Atlas initiative that aims to map every cell type in the human body, provides key new insights that could lead to better Crohn’s disease management and treatment.

“Crohn’s disease can be particularly aggressive and more treatment-resistant in children, so there’s a real need to understand the condition when it affects them and perhaps come up with childhood-specific treatments,” said research lead Matthias Zilbauer, MD, PhD, lecturer in the department of pediatrics at the University of Cambridge and honorary consultant in pediatric gastroenterology at Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust. Zilbauer and colleagues reported on their findings in Developmental Cell, in a paper titled, “Single-cell sequencing of developing human gut reveals transcriptional links to childhood Crohn’s disease.”

Development of the human intestine is a highly complex process that requires the orchestrated interaction of differentiating cell types, the authors wrote. Importantly, environmentally triggered changes in early development have been implicated in immune-mediated disorders including inflammatory bowel diseases (IBD). “Furthermore, a number of studies have reported a link between early fetal intestinal epithelial cell dynamics and IBD, suggesting that fetal-like transcriptional program may re-appear in the intestinal epithelium of IBD patients.” Having a much better understanding of physiological intestinal development will thus be critical to the ability to prevent and treat such conditions, the team noted. However, subtle differences between gut development in mice and in humans, and a lack of access to human fetal and embryonic tissue, have meant that scientists only have a “rudimentary” understanding of the processes involved in humans.

Crohn’s disease is a type of inflammatory bowel disease that affects about one in every 650 people in the U.K. Incidence of the disorder has increased dramatically in recent decades, and especially in children, who can suffer very aggressive symptoms including abdominal pain, diarrhea, and fatigue. This lifelong condition can have major life implications, as the cause is not understood, treatments often don’t work, and there is no cure.

For their reported studies, Zilbauer and colleagues carried out single-cell RNA sequencing to look at gene expression in individual cells of the developing human gut in human embryos six to ten weeks after conception. Their studies, focused on the intestinal epithelium, the inner lining of the gut, showed that the cells there divide constantly at this early stage, guided by messages from other cell types. This communication allows the gut to grow and form the structures needed for good gut function later in life.

The team also analyzed gut tissues from children, aged between four and twelve years, who had Crohn’s disease, and tissue from healthy children without the disorder. “In total, we generate single-cell transcriptomes of ~90,000 primary human intestinal cells providing a rich resource and a detailed roadmap,” they wrote. Results from their analysis of gut tissues from the Crohn’s disease patients and healthy controls indicated that some of the cellular pathways that are active in the epithelium of the fetal gut are then reactivated in the children with Crohn’s disease, but not in healthy children of a similar age.

Emerging intestinal villi with green stem cells supporting their growth [Kenny Roberts & Sophie Pritchard, Wellcome Sanger Institute]
“Previous studies in mice have linked epithelial cell properties in the inflamed gut to the physiological status observed in early fetal development,” the authors wrote. “Here, we provide evidence in humans that regenerating CD epithelium shares transcription factor programs otherwise present only in fetal epithelium.” Zilbauer further commented, “Our results indicate there might be a reprogramming of specific gut cell functions in Crohn’s disease. We don’t know whether this is the cause of the disease or a consequence of it, but either way, it is an exciting step in helping us to better understand the condition.”

The findings do shed light on some of the fundamental molecular mechanisms of human gut development. The team also found that lab-grown “mini-guts” undergo similar individual cellular changes to those inside a developing fetus. This implies that lab-grown models represent an accurate tool for future research into very early gut development and associated diseases.

“This study is part of the international Human Cell Atlas effort to create a ‘Google map’ of the entire human body. With single-cell RNA sequencing we can look at any tissue and identify the individual cell types it’s made up of, the function of those cells, and even identify new cell types,” said Sarah Teichmann, PhD, at the Wellcome Sanger Institute, and co-chair of the Human Cell Atlas Organising Committee, whose expertise enabled analysis of the huge amount of data generated by this technique.

She added: “A complex tissue like the gut contains different cell types, and these ‘talk’ to each other—the function of one cell affects the function of another. That’s particularly important in the early stages of gut development, and something we can interrogate using computational analyses of single-cell RNA sequencing data.”

The researchers have made their data openly available at www.gutcellatlas.org, creating a valuable resource for further research and drug discovery targeted at childhood Crohn’s disease. “… we provide a detailed single-cell map of the human gut during embryonic, fetal and pediatric health as well as inflammatory disease, and dissect transcriptional changes in epithelial cell dynamics during intestinal life,” the scientists wrote.

“From my own experience we’re diagnosing Crohn’s Disease in younger and younger children, some even under the age of five—it’s very much an emerging disease,” Zilbauer said. “It’s a really nasty, lifelong condition, and when children are diagnosed, the whole family is affected. We are determined to advance our knowledge in this area, and hopefully, improve the lives of these children in the future.”

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