Swedish scientists map spatial transcriptome of colonic mucosal healing for the first time

Researchers at Karolinska Institutet in Sweden have used a technique called spatial transcriptomics to analyze gene expression in mouse colons and create a map of where each gene is located in the tissue.
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When they superimposed previously known human transcriptome data onto the atlas, the researchers gained new insights into inflammatory bowel disease (IBD)

The intestinal barrier consists of a complex network of cells that define a highly compartmentalized and specialized structure
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The gut relies on constant regeneration of the intestinal epithelium to maintain homeostasis

So the researchers used spatial transcriptomics to map the gene activity of individual cells in the mouse colon
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According to them, this is the first time scientists have looked at the gene expression landscape of the entire gut, both in health and in recovery from injury

Corresponding author Eduardo J.
Villablanca of Karolinska Institutet said: "Spatial transcriptomics-driven visualization allows us to uncover several previously unknown aspects, such as the fact that the colon is divided into more segments than previously thought.

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The researchers also combined these results with known transcriptomic data from human tissues and found that certain gut cells are located in the same location in mice and humans, which enables the model to be used to study human diseases such as IBD, Helps to understand how different diseases affect the colon
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In an earlier study, Eduardo J.
Villablanca's team showed that ulcerative colitis can be divided into two subtypes with different gene expression profiles
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Based on the new atlas, they found that genes for more difficult-to-treat disease subtypes were found in more severely damaged tissues

"Similarly, genetic maps can be used to see where human cells are activated in the colon, which has important implications for the development of new therapies and drugs," Villablanca said
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Spatial transcriptomics technology was developed by the Swedish Life Sciences Laboratory (SciLifeLab)
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It enables the observation of gene expression in tissues

"We wanted to use the same method to create a similar map for all digestive organs, from the mouth to the rectum," explains Villablanca
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"Our goal was to create a reference map for gene expression in all these tissues

Genetic mapping of the entire digestive organ can be useful in many ways, such as exploring the links between gut bacteria and cellular gene expression, and better understanding how different diets affect its various functions

The research was carried out at Karolinska Institutet and was supported by grants from the Swedish Research Council, the Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (Formas), the Swedish Cancer Society and the Knut and Alice Wallenberg Foundation

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Parigi, SM, Larsson, L.