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PID: hpt/lnx 1.9.0-cur 2019-01-08
TID: hpt/lnx 1.9.0-cur 2019-01-08
 Scientists link genes to diet in inflammatory bowel disease 
 A study in mice identifies candidate genes associated with bowel
inflammation caused by a high-fat diet 

  Date:
      July 5, 2023
  Source:
      eLife
  Summary:
      A study of the genetic variation that makes mice more susceptible
      to bowel inflammation after a high-fat diet has identified candidate
      genes which may drive inflammatory bowel disease (IBD) in humans.


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FULL STORY
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A study of the genetic variation that makes mice more susceptible to
bowel inflammation after a high-fat diet has identified candidate genes
which may drive inflammatory bowel disease (IBD) in humans. The findings
are published as a Reviewed Preprint in eLife.

Described by the editors as a fundamental study, the work provides a
framework for using systems genetics approaches to dissect the complex
mechanisms of gut physiology. The authors show how it is possible to use
genetically diverse but well-characterised mice to interrogate intestinal
inflammation and pinpoint genes influenced by the environment - in this
case, a high-fat diet - and identify potential treatment targets for IBD
in mice and humans. The editors describe the strength of the analyses
as compelling and add that, as a resource, it will be useful for linking
genetic variations and diet to gut- related disorders.

It is well established that a high-fat diet can increase the risk of IBD.

However, the impact of diet varies between individual people, suggesting
an interplay with genetic factors. More than 200 risk genes have been
identified for IBD, but there is still no effective treatment, and it is
therefore important to understand the gene-by-environment interactions
underpinning the inflammation that eventually evolves into IBD.

"Differences in the clinical presentation of IBD among patients, as
well as diversity in diet and lifestyle, render human genetic studies
challenging," explains lead author Xiaoxu Li, a Doctoral Research
Assistant at the Institute of Bioengineering, E'cole Polytechnique
Fe'de'rale de Lausanne (EPFL), Switzerland. "Genetically diverse
populations of mice allow us to mirror the differences in human
populations, while controlling several environmental factors, such as
temperature and diet, when exploring the genetic modulators of IBD in the
laboratory."  Li and colleagues used mouse genetic reference populations
(GRPs) to map the genetic factors that are important in IBD induced by a
high-fat diet. They measured the levels of gene expression in the colons
of 52 mice fed with either a chow or a high-fat diet and identified a
subset of mice that were more susceptible to high-fat-diet-induced
intestinal inflammation. Moreover, they found that levels of a
pro-inflammatory cytokine called interleukin-15 were increased in the
mice more likely to develop IBD, while levels of the anti- inflammatory
cytokine, Interleukin-10, were decreased. This indicates that changes in
the levels of genes associated with IBD reflect the general inflammatory
status of mice.

After classifying different mouse strains based on their likelihood of
developing IBD-like genetic signatures, the team explored this further
using gene co-expression network analysis. This identified two distinct
modules (clusters) of genes that are related to known genetic signatures
of human IBD.

Next, they looked at the function of these genes and how they are
controlled.

Both IBD-associated modules largely consisted of immune response-related
genes, including those known to be involved in Crohn's disease, and
the team identified the likely regulators of the expression of these
genes. But the genetic drivers behind the different susceptibility in
the mice were still elusive.

To find the candidate genes that influence gut inflammation specifically
following a high-fat diet, they performed QTL analysis to identify
quantitative trait loci (QTL) - regions of genes that interact with the
environment to impact the observable trait data. This revealed a QTL
that is related to chronic intestinal inflammation in mice.

To see whether genes under this QTL could play a role in human IBD,
the team then cross-checked their findings with risk genes for IBD by
conducting an analysis using genome-wide association study data from UK
Biobank*. They identified two plausible gene candidates, called EPHA6
and MUC4. In addition, using publicly available genetic variation data
for IBD, Crohn's disease and ulcerative colitis, they found evidence to
suggest that increased expression of the MUC4 gene in part of the colon
may increase the risk of IBD in humans.

A limitation of this analysis is that there were no mechanistic
investigations or studies that directly provide a causative link between
the candidate genes and IBD. The results are primarily observational
and correlative, but they provide a dataset that generates hypotheses
that can be studied further.

"Our results point to important potential roles of two gene candidates
in gut chronic inflammation that may lead to inflammatory disorders,"
says senior author Johan Auwerx, a Professor at the Institute of
Bioengineering, EPFL. "Our systems genetics approach using GRP mice where
the genetic backgrounds are known and the environment can be controlled
enables the prioritisation of candidate genes in a complex disease which,
when combined with human genome- wide association studies from UK Biobank,
are generalisable to human patients and may have clinical value."
    * RELATED_TOPICS
          o Health_&_Medicine
                # Gastrointestinal_Problems # Genes # Obesity #
                Cholesterol # Diet_and_Weight_Loss # Colitis #
                Crohn's_Disease # Nutrition
    * RELATED_TERMS
          o Irritable_bowel_syndrome o Coeliac_disease o Constipation
          o Genetics o Heritability o Personalized_medicine o
          Gastroenteritis o South_Beach_diet

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Journal Reference:
   1. Xiaoxu Li et al. Genetic and dietary modulators of the inflammatory
      response in the gastro-intestinal tract of the BXD mouse genetic
      reference population. eLife, 2023 DOI: 10.7554/eLife.87569.2
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Link to news story:
https://www.sciencedaily.com/releases/2023/07/230705115125.htm

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