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Deciphering the molecular language of the small intestine

Coloured scanning electron micrograph (SEM) of microvilli from the small intestine. These tiny structures help the cells lining the small intestine to absorb nutrients from digested food.© STEVE GSCHMEISSNER/SCIENCE PHOTO LIBRARY/Getty Images

What will you explore in your GGGH project?

Our main goal is to begin deciphering the molecular communication between bacteria (and the small molecules they secrete) and host cells in the small intestine. We’re particularly interested in enteroendocrine cells — cells found in the lining of the small intestine and throughout the intestinal tract — and how the small-intestine microbiome prompts them to release hormones. We also want to explore how this communication allows gut bacteria to alter physiology throughout the body. We know that gut bacteria affect biological processes in distal places such as the brain and skeletal muscles. I believe that bacterial communication with enteroendocrine cells is a major mechanism. These cells secrete hormones and neurotransmitters, and they also talk to neurons, sending signals across the body. We know there are physical interactions, where bacteria adhere to host cells. There are also chemical-signaling interactions, where intestinal cells sense and react to small molecules produced by microbes. We don’t yet understand the full context or implications of this molecular language in the small intestine. We hope to begin probing which small molecules the enteroendocrine cells respond to, which bacteria produce these molecules, which receptors they bind to, and how that translates to changes in biological processes. Our hope is to provide valuable novel therapeutic targets, not just for metabolic disorders, but also for neuropsychiatric conditions, and disorders influenced by the microbiome.

What cells and molecules will you focus on?

The small intestine is an incredibly dynamic environment, and we know that diet is a key influence on small-intestine activity. We also know there is a rich diversity of enteroendocrine cells in the small intestine, and that the chemical landscape is very interesting. There are different types of enteroendocrine cells, each with its own specialized function. Most commonly, they each secrete a different hormone in response to external prompts such as diet. For this project, we’re interested in two specific hormones secreted by small-intestine enteroendocrine cells: glucagon-like peptide 1 (GLP1) and peptide tyrosine tyrosine (PYY). Both hormones are released after eating, and mediate our sense of satiation, essentially telling us when we should stop eating. They also help regulate glucose homeostasis, and are key players in maintaining healthy metabolism. Disruption to these hormones has been implicated in metabolic diseases, and so it seems pertinent to start with these, given the considerable burden of metabolic disease on global health services at present. However, we don’t know exactly what mechanisms are involved in inducing and regulating hormone secretion, which is what we will explore.

What steps will you take to achieve your aims?

We are starting at the molecular level, and from there we will add layers of complexity to learn more about the bigger picture. We will use a simplified version of the small intestine in the lab in the form of an organoid. An organoid is a three-dimensional, miniaturized model of an organ that mimics its activity and replicates the interactions that occur between and within cells. We will use small-intestine organoids to monitor interactions between host enteroendocrine cells and the small-intestine microbiota population. In particular, we will use single-cell RNA sequencing to probe how each individual cell type responds to bacteria and their associated small molecules. We will then use CRISPR screening to examine which receptors are responding to which signals, and define those factors involved in mediating host responses of interest — such as the secretion of the two hormones mentioned earlier.

Why is developing a small-intestine organoid helpful in this context?

Organoids are essential because it’s impossible to grow most types of enteroendocrine cells in a standard culture. Organoids allow you to grow and enrich cells within their physiological context, and other groups have developed organoids models of all regions of the intestine. Organoids also allow us to look at responses of enteroendocrine cells at much higher throughput than mouse models, which many previous studies probing enteroendocrine cells have used. Organoids are constructed through the differentiation of human pluripotent stem cells — this is a targeted way of generating the main cell types of interest, which then assemble themselves into a functioning miniature organ. An important element to consider is that the small intestine is a rapidly changing environment inside humans, and it is influenced by a multiplicity of factors. My vision is to use our organoid in vitro model as a reductionist model — it’s a starting point, but not a definitive end point. We can use it to identify key molecules and receptors before exploring them further in in vivo models in future.

How might the results inform future therapies?

We’re designing our in vitro experiments to be as informative as possible, exploring a wide range of interactions, not just for therapeutics but also for improving our understanding of basic biology. But it’s important that we also prioritize, which is why we’re looking at GLP1 and PYY in this project. We might find specific molecules — bacterial or dietary — or specific receptors that trigger production of these hormones and we can then use classical drug-discovery techniques to explore ways of optimizing these interactions to improve glucose control, for example. Alternatively, we may find links between diet and host responses, which may lead to the design of dietary interventions. Longer term, there’s the possibility of engineering microbes that could reduce or degrade unwanted substances, or optimize the activity of enteroendocrine cells in specific circumstances. This might give us more temporal and spatial control over the gut microbiome. Ultimately, we need big clinical trials on humans, but they require well-defined targets.

What are your hopes for future research?

Hopefully, this study will provide a blueprint for us to look at molecular communication in far greater detail, not just between gut microbes and enteroendocrine cells, but also between other cell types. My broader aim is to continue to develop techniques that enable us to decipher this complex molecular language and learn about how this communication shapes us.


© Marco Jost

Marco Jost is an assistant professor of microbiology at Harvard Medical School in Boston, US, where he set up the Jost Lab in April 2021. His postdoc with Jonathan Weissman and Carol Gross at the University of California San Francisco involved developing tailored CRISPR screening techniques, which he used to begin exploring the gut microbiome in collaboration with Michael Fischbach and colleagues. The Jost Lab will use single-cell RNA sequencing and CRISPR technologies to improve understanding of molecular communications in the gut and how this influences physiology throughout the body.

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