Another molecular clue in the mysterious influence of microbiota in the gut

By focusing on small molecules called microRNAs in stem cells of the intestine, UNC School of Medicine researchers have proposed a new mechanism by which gut microbes might help keep us healthy or make us sick.

Media Contact: Matt Englund, (984) 974-1144

January 18, 2017

CHAPEL HILL, NC – The inner lining of our intestine is a protective layer of epithelial cells that bars the entry of harmful toxins and pathogens, while allowing nutrients through. This layer constantly interacts with naturally occurring bacteria – the gut microbiota – the makeup of which can affect the health of the intestine including the integrity of the epithelium itself. Stem cells, which reside in the base of the intestinal epithelium called the crypt, rapidly divide to generate a new intestinal epithelial layer every few days, making it the most rapidly renewing tissue in the entire body.

Focusing on the expression of microRNAs (miRNAs) in several different specialized cell types of the intestinal epithelium, including intestinal stem cells, researchers at the UNC School of Medicine are proposing a new mechanism for how the gut microbiota may help control the function of intestinal stem cells and thereby the health of the intestinal epithelium. The findings were published last week in The Journal of Biological Chemistry.

miRNAs are small molecules of genetic information that are not translated into proteins but still can play important roles in determining where, when, and how much other genes are expressed.

“Several studies have established that gut microbiota control various aspects of intestinal physiology,” said Praveen Sethupathy, PhD, senior author and assistant professor of genetics at UNC. “Notably, microbial colonization of germ-depleted mice can promote proliferation of the cells in the intestinal crypt, which is critical for the maintenance of normal function of the entire intestinal epithelium.  But how this happens – the mechanisms behind it – are still being teased out.  Our research suggests that miRNAs may be key players.”

Sethupathy’s lab used mouse models and functional genomics techniques to create an intestinal map of miRNAs in order to determine which miRNAs in which intestinal epithelial cell types were most sensitive to the presence of gut microbiota. The results led the team to more closely consider one particular miRNA, miR-375, in intestinal stem cells.  They demonstrated that the presence of gut bacteria leads to dramatically lower levels of miR-375 in intestinal stem cells. They then conducted experiments using small molecules called locked nucleic acids in 3D mini-guts grown in culture (called enteroids) to propose a new role for miR-375 in intestinal stem cells.

“We can now test the function of many other miRNAs very quickly using just one mouse, by harvesting and growing the intestinal cells in culture as enteroids, which are thought to closely mimic normal intestinal epithelial behavior and function,” added Bailey Peck, PhD, who was first author on the study.

This is the first-ever definition of miRNA expression across specialized cell types of the intestinal epithelium and demonstrates that miRNAs in intestinal stem cells are more sensitive to the presence of gut microbiota than in any other intestinal epithelial cell type included in the study.

“Defects in intestinal stem cell function can lead to intestinal epithelial failure, and possibly to a variety of crippling gastrointestinal disorders,” explained Sethupathy.  “So understanding how microbiota help control intestinal stem cells can offer critical insights into the mechanisms that keep the intestine healthy.”

Because the intestinal epithelium serves such an important function in maintaining health, the findings open up several avenues for the development of new therapeutic targets.

“miRNAs have emerged as attractive therapeutic targets in a wide range of diseases,” Sethupathy said.  “Small molecules have been developed that target miRNAs of interest with a high level of specificity and potency.  A key next step in the field is to develop approaches for targeted delivery of these small molecules to specific cell types of interest such as intestinal stem cells.”

The findings of the study also raise several new questions for future research.  Specifically, are there other miRNAs that work together with mIR-375 in intestinal stem cells?  How do gut microbiota control miRNAs in intestinal stem cells?  And are there specific bacteria that specialize in communicating with the stem cells?

“Dr. Peck’s capable work and perseverance on this multi-disciplinary project, as well as a very productive scientific partnership with Prof. Kay Lund and her group, and the expertise of the outstanding UNC gastrointestinal biology research community, has helped cement a new avenue of research in our lab that we anticipate will continue to bear fruit in the years to come,” said Sethupathy. “We are particularly grateful for the support and assistance provided by the UNC GI Stem Cell Group and the UNC Gnotobiotic Core Facility.”

The experiments during this research were led by Bailey Peck, PhD, a former genetics and molecular biology graduate student in Sethupathy’s lab who is now a postdoctoral researcher at the University of Michigan. Other contributors include Amanda Mah, PhD, Wendy Pitman, PhD, senior bioinformatics analyst in the Sethupathy lab, Shengli Ding, PhD, and P. Kay Lund, PhD, professor of cell biology and physiology.

 Funding and support for this work was provided by numerous sources: UNC Genetics and Molecular Biology T32 Training Grant, UNC IMSD Diversity Fellowship, National Institutes of Health Pre-doctoral F31 Fellowship, UNC Center for Gastrointestinal Biology and Disease Pilot Grant, National Institute of Diabetes and Digestive and Kidney Diseases R01 Grant, and the American Diabetes Association Pathway Program Research Accelerator Award.

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