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Characterisation of gene and pathway expression in stabilised blood from children with coeliac disease
Hanna Gustafsson Bragde1,2, Ulf Jansson3, Mats Fredrikson2
1Laboratory Medicine, Region Jönköping County, Jönköping, Sweden hanna.gustafsson.bragde@rjl.se.
Insights
Gene expression in stabilized whole blood shows promise for diagnosing coeliac disease (CD) by analyzing pathways, not single genes. This blood-based approach could offer a less invasive alternative to biopsies for CD diagnosis and monitoring.
Area of Science:
- Immunology
- Genetics
- Molecular Biology
Background:
- Coeliac disease (CD) diagnosis in children often relies on high levels of tissue transglutaminase autoantibodies (anti-TG2) or intestinal biopsy.
- Stabilized whole blood preserves gene expression, making it a potential sample for diagnostics.
- Investigating gene expression in stabilized blood could offer a less invasive diagnostic method for CD.
Purpose of the Study:
- To explore gene expression in stabilized whole blood for diagnosing and monitoring coeliac disease.
- To identify potential gene expression biomarkers and pathways involved in CD pathogenesis.
- To assess the feasibility of a pathway-focused gene expression panel for CD diagnostics.
Main Methods:
- RNA sequencing was performed on stabilized whole blood samples from active CD, non-CD, and treated CD groups.
- Gene set enrichment analysis (GSEA) was used to identify differentially expressed pathways.
- GSEA results from blood were compared with those from small intestinal biopsies.
Main Results:
- No single gene showed differential expression between sample groups.
- GSEA identified significant pathway differences in active CD, including inflammatory response and cell regulation pathways.
- Common pathways between stabilized blood and intestinal biopsies included type I interferon response and viral defense.
Conclusions:
- Stabilized whole blood is not suitable for single-gene based CD diagnostics.
- Pathway-focused gene expression panels using stabilized blood may be feasible for CD diagnostics, warranting further research.
Introduction:
A coeliac disease (CD) diagnosis is likely in children with levels of tissue transglutaminase autoantibodies (anti-TG2) >10 times the upper reference value, whereas children with lower anti-TG2 levels need an intestinal biopsy to confirm or rule out CD. A blood sample is easier to obtain than an intestinal biopsy sample, and stabilised blood is suitable for routine diagnostics because transcript levels are preserved at sampling. Therefore, we investigated gene expression in stabilised whole blood to explore the possibility of gene expression-based diagnostics for the diagnosis and follow-up of CD.
Design:
We performed RNA sequencing of stabilised whole blood from active CD cases (n=10), non-CD cases (n=10), and treated CD cases on a gluten-free diet (n=10) to identify diagnostic CD biomarkers and pathways involved in CD pathogenesis.
Results:
No single gene was differentially expressed between the sample groups. However, by using gene set enrichment analysis (GSEA), significantly differentially expressed pathways were identified in active CD, and these pathways involved the inflammatory response, negative regulation of viral replication, translation, as well as cell proliferation, differentiation, migration, and survival. The results indicate that there are differences in pathway regulation in CD, which could be used for diagnostic purposes. Comparison between GSEA results based on stabilised blood with GSEA results based on small intestinal biopsies revealed that type I interferon response, defence response to virus, and negative regulation of viral replication were identified as pathways common to both tissues.
Conclusions:
Stabilised whole blood is not a suitable sample for clinical diagnostics of CD based on single genes. However, diagnostics based on a pathway-focused gene expression panel may be feasible, but requires further investigation.
