Now, researchers at the Broad Institute of MIT and Harvard and Massachusetts General Hospital have analyzed the entire mouse intestine, mapping gene expression and cell states and location in the healthy gut and in response to perturbations such as inflammation. They identified tight regulation of cell types and states in different regions of the organ, as well as a unique segment of the colon that is controlled by immune signals. The findings, which appear in Nature, reveal the surprising adaptability and resilience of the intestine to perturbations and highlight the importance of considering how cell processes are regulated and vary across different parts of a tissue or organ.

“The intestine and in particular the colon has been studied for decades but it hasn’t been characterized in this way before, and that both forces us to reevaluate many different studies and opens up a window for future research,” said Toufic Mayassi, a co-first author on the study along with Chenhao Li. Mayassi and Li are postdoctoral researchers in the lab of Ramnik Xavier, who is a core institute member at the Broad, member of the Center for Computational and Integrative Biology at Massachusetts General Hospital (MGH), and senior author of the study.

“This work illustrates that you really have to integrate the spatial relationships governing a given organ into your thinking, and we hope our study provides a platform and framework that helps put both previous and future discoveries in context,” Mayassi said.

Xavier is the director of Broad’s Immunology Program, as well as the Kurt J. Isselbacher Professor of Medicine at Harvard Medical School, director of the Center for Computational and Integrative Biology and member of the Department of Molecular Biology at MGH, and co-director of the Center for Microbiome Informatics and Therapeutics at MIT.

“We’ve built a blueprint of the entire gut, and that’s a remarkable achievement,” said Xavier. “We now have a way of studying the whole organ, examining the effect of genetic variants and immune responses associated with diet, the microbiome, and gastrointestinal disease, and designing many other experiments.”

Mapping the intestine

Many previous studies of the gut looked at cells or organ-like assemblies of cells in a dish. While such approaches provide a controlled environment to study the function of specific genetic variants involved in disease, they don’t illustrate how cells from different parts of an intact organ interact to bring about disease.

In 2021, Mayassi, who spent his PhD studying immune responses in the intestine, teamed up with Li, a computational biologist, to build a comprehensive map of gene expression across the entire mouse small intestine and colon using spatial transcriptomics and computational approaches.

To the researchers’ surprise, the spatial composition of the intestine — the relative location of various cell types and the genes they express — remained relatively stable when certain factors changed. It stayed the same in animals with and without gut microbiota and in tissue collected at night or during the day, suggesting that neither the microbiome nor circadian rhythms impacted the spatial landscape.

The intestine also showed signs of resilience. When Mayassi treated the animals with a molecule known to induce inflammation, gene expression and cell spatial distribution changed but showed signs of returning to normal a month later, and had almost entirely recovered by three months. The findings suggest that the gut’s ability to bounce back from changes brought about by inflammation could be critical to intestinal health and function.

“As a computational biologist, it is exciting to be involved in generating and exploring such a unique dataset,” Li said. “It opens the door to developing tools for analyzing spatial data and informs the design of future studies on the small and large intestine.”

Immune control

Though the intestine was stable to many influences, unique niches within the organ were affected by the gut microbiota and showed signs of adaptation. Mice that had a normal microbiome expressed unique genes in a specific region of the colon compared to germ-free mice. Using single-cell RNA sequencing, the authors found that the changes occurred in three structural cell types. In particular, goblet cells — cup-shaped cells that secrete mucus — expressed those genes only in the presence of ILC2s, a kind of immune cell.

Next, the researchers plan to apply their method to study how other factors including sex, diet, food allergies, and genetic risk factors for conditions such as inflammatory bowel disease impact the intestine’s spatial landscape. They also hope to elucidate the extent to which the findings in mice correlate with spatial control in the human gut.