Unravelling intestinal inflammation: from Celiac Disease genotype to autoimmunity.

About 50% of patients visiting gastroenterological clinics have symptoms that
can be associated with a diversity of autoimmune diseases, including Celiac
Disease (CeD) and Irritable Bowel Syndrome (IBS). We study the patho-mechanisms
involved in CeD with the final aim to improve the diagnosis, prevention and
treatment of CeD patients. CeD is a very common autoimmunity (incidence 1%)
that is triggered by dietary gluten (the storage protein of wheat, barley and
rye). CeD only develops in patients with a genetic susceptibility but the
nature of all the genes involved in diseases susceptibility remains to be
elucidated. We do know one major genetic risk factor (HLA) and 39 minor risk
factors. The current diagnosis in CeD is based on symptomatic, serologic and
histo-pathological features, but still only 1 out of 8 CeD patients is properly
diagnosed. So far genetics, based on HLA, is only used to exclude CeD. The
under-diagnosis of CeD is caused by the wide variety of clinical symptoms and
the overlap with other phenotypes like IBS (incidence estimated between 10-30%;
Roberts et al., 2013). The major consequence of misdiagnosing CeD is that
patients do not follow a gluten-free diet, which severely increases the risk of
complications and increases mortality.
We have been studying the genetics of CeD for over 15 years and have
contributed to elucidating approx. 50% of the genetic factors involved in CeD
(contributed by the 40 genetic factors mentioned above). The proposed studies
will help CeD patients in two ways: (1) we will identify novel genetic markers
that will improve diagnosis and predict who is at-risk for developing disease
(and thereby contribute to disease prevention), (2) the genetic insights
obtained, enhance our understanding of the disease process which ultimately
will lead to the development of new ways to treat CeD.
We are currently at a stage at which we can start to translate genetic findings
into insights in the disease process using state-of-the-art bioinformatic
approaches, but for this we do need to study CeD patients and their immune
cells (as CeD is an autoimmune disease) in much more detail. In particular we
have to understand how multiple CeD genetic risk factors are jointly
deregulating immune cells and how this eventually leads to disease. Since CeD
manifests in the intestine it is also possible that there is an interaction
between intestinal immune cells and the gut microbiome.
In summary, in order to be as succesful as possible we want to analyze the
genetic profile of the patients, the symptoms involved in the disease, the
activation potential of the patient's immune cells, metabolites associated with
the disease, and the microbiome of the subjects. These different layers of
information will then be integrated by bioinformatic analysis, to obtain novel
insights into the pathologie of Celiac Disease.

The primary aim of the current proposal is to get a better understanding of how
CeD risk genes contribute to disease aetiology. To achieve this, we will apply
a holistic approach in which we will study the behaviour of immune cells and
the microbiome in CeD patients and compare that to non-patients using *omics*
technology (i.e. the full repertoire of all transcripts, cytokine profiles,
proteins, metabolites etc.) in the background of the genetic profile of each
individual. To generate this information we for instance have to profile
different immune cells from patients and controls. The datasets will be
analysed and integrated using bioinformatics to develop insights into disease
mechanism. The technology we apply can also be used for disease prediction.
Hence the secondary aims are to (a) develop biomarker profiles that will
improve diagnosis (preferentially before full blown manifestation of the
disease), (b) to investigate whether disease specific biomarkers affect the
biology of the cells and tissues involved in the disease, and (c) to
investigate the commonalities and specificities of CeD when compared with other
intestinal diseases. As we have to integrate information on genetics, immune
cells and microbes, a panel of biomaterials (isolated from blood, urine, stool
and buccal smears) will be sampled using non-invasive techniques (the most
invasive being blood sampling). From these samples genomic, transcriptomic,
epigenetic, serological, metabolomic, and microbiomic data will be generated
and analysed. This will be complemented with phenotypic data acquired by
examination of the study subjects at the time of presentation, medical records,
and from questionnaires that the subjects will be asked to complete.

This is a non-therapeutic study. Patients that visit the out-patient clinic of
the Gastroenterology and Hepatology department of the UMCG will be recruited.
Three extra tubes of blood (10ml) will be collected at the scheduled diagnostic
venepuncture during their regular visit to the outpatient clinic of the
department of Gastroenterology and Hepatology. Additionally, a buccal smear
will be taken for identification of the microbiome of the oral cavity and the
subject will be requested to exhale over a filter that will capture volatile
organic compounds (metabolites). All contributors will be requested to provide
a stool and urine sample which will be collected at home, and additionally to
fill in a questionnaire.The data will be generated and analysed at the
department of Genetics of the UMCG. Currently we are performing identical
analyses in our *LifeLinesDeep* cohort, for which we are profiling 1.500
subjects in an identical manner. The LifeLinesDeep data will also provide the
base-line values for our patient-derived data.

Three extra tubes of blood (10ml) will be collected at the scheduled diagnostic
venepuncture during the regular visit to the outpatient clinic of the
department of Gastroenterology and Hepatology. Additionally, a buccal smear
will be taken and the subject will be requested to exhale in a bag. All
contributors will be requested to provide a stool and urine sample which will
be collected at home, and additionally to fill in a questionnaire.
The risk and burden associated with these procedures is negligible.

The study will not provide an immediate benefit for the participants, but the
results will help in the future with improving diagnostics and treatment, and
hopefully prevention of CeD.