Colonic gene mapping gives insights into intestinal diseases

Date:
February 11, 2022
Source:
Karolinska Institutet
Summary:
Using a technique called spatial transcriptomics, researchers have
analyzed the gene expression in the mouse colon and created a map
showing where in the tissue individual genes are expressed. When
they superimposed previously known human transcription data onto
the map, the researchers gained new insights into inflammatory
bowel disease (IBD).



FULL STORY ========================================================================== Using a technique called spatial transcriptomics, researchers at
Karolinska Institutet in Sweden have analysed the gene expression in the
mouse colon and created a map showing where in the tissue individual
genes are expressed. When they superimposed previously known human transcription data onto the map, the researchers gained new insights
into inflammatory bowel disease (IBD). The study is published in the
journal Nature Communications.


==========================================================================
The group used a technique known as spatial transcriptomics (ST) to map
the gene activity of individual cells in the murine colon. According to
the researchers, this is the first time anyone has been able to visualise
the gene expression landscape of the entire intestine, in health and
recovery after injury.

"Our spatial transcriptomics-driven visualisation enabled us to discover several previously unknown aspects, such as that the colon is divided
into more segments than once thought," says the study's corresponding
author Eduardo J.

Villablanca, docent at the Department of Medicine, Solna at Karolinska Institutet.

When the results were combined with known transcription data from human
tissue, the scientists noticed that the location of certain intestinal
cells was the same in both mice and humans, which makes the model a tool
for understanding how different diseases, such as IBD, affect the colon.

In an earlier study, Eduardo J. Villablanca's research group showed
that ulcerative colitis can be divided into two subgroups with different
gene expressions. With reference to the new map, they were able to show
that the genes for the more difficult to treat forms of the disease were
found in tissue that was also more damaged.

"Similarly, the gene map can be used to see where in the colon human
cells are active, which can make a significant contribution to the
development of new treatments and drugs," Villablanca says.

Spatial transcriptomics was developed at SciLifeLab by scientists from
KTH Royal Institute of Technology and Karolinska Institutet. It allows
the visualization of gene expression in the tissue. However, to visualize
a long tubular organ like the colon, the researchers behind this study
applied the technique in a novel way. By rolling up the colon like
a Swiss roll, they managed to fit and map the entire gene expression
landscape of a long organ.

"We now want to use the same method to create a similar atlas for
all digestive organs, from the mouth to the rectum," Villablanca
explains. "Our aim is to create a reference map for the gene expression of
all these tissues." A gene atlas of the entire digestive organ will be
useful in many ways, such as for exploring the link between gut bacteria
and cellular gene expression, and for gaining a better understanding of
how different diets affect its various functions.

The study was conducted at Karolinska Institutet with financial support
from, among others, 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.

Some of the authors have reported declarations of interest: Eduardo J.

Villablanca has received research funding from the pharmaceutical
company F.

Hoffmann-La Roche; and Camilla Engblom, Ludvig Larsson and Joakim
Lundeberg are scientific advisors to 10X Genomics, which acquired the
company Spatial Transcriptomics in 2018.

========================================================================== Story Source: Materials provided by Karolinska_Institutet. Note: Content
may be edited for style and length.


========================================================================== Journal Reference:
1. Sara M. Parigi, Ludvig Larsson, Srustidhar Das, Ricardo O. Ramirez
Flores, Annika Frede, Kumar P. Tripathi, Oscar E. Diaz, Katja Selin,
Rodrigo A. Morales, Xinxin Luo, Gustavo Monasterio, Camilla Engblom,
Nicola Gagliani, Julio Saez-Rodriguez, Joakim Lundeberg, Eduardo J.

Villablanca. The spatial transcriptomic landscape of the healing
mouse intestine following damage. Nature Communications, 2022; 13
(1) DOI: 10.1038/s41467-022-28497-0 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2022/02/220211102636.htm

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