Characterisation of gene and pathway expression in stabilised blood from children with coeliac disease
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 t...
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BMJ Publishing Group
2020-12-01
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| Series: | BMJ Open Gastroenterology |
| Online Access: | https://bmjopengastro.bmj.com/content/7/1/e000536.full |
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| author | Mats Fredrikson Hanna Gustafsson Bragde Ulf Jansson Ewa Grodzinsky Jan Söderman |
| author_facet | Mats Fredrikson Hanna Gustafsson Bragde Ulf Jansson Ewa Grodzinsky Jan Söderman |
| author_sort | Mats Fredrikson |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-ed7b00f1236b4f939887ce3dc7036270 |
| institution | DOAJ |
| issn | 2054-4774 |
| language | English |
| publishDate | 2020-12-01 |
| publisher | BMJ Publishing Group |
| record_format | Article |
| series | BMJ Open Gastroenterology |
| spelling | doaj-art-ed7b00f1236b4f939887ce3dc70362702025-08-20T02:39:13ZengBMJ Publishing GroupBMJ Open Gastroenterology2054-47742020-12-017110.1136/bmjgast-2020-000536Characterisation of gene and pathway expression in stabilised blood from children with coeliac diseaseMats Fredrikson0Hanna Gustafsson Bragde1Ulf Jansson2Ewa Grodzinsky3Jan Söderman4Department of Biomedical and Clinical Sciences and Forum Östergötland, Faculty of Medicine and Health Sciences, Linköping University, Linköping, SwedenLaboratory Medicine, Region Jönköping County, Jönköping, SwedenDepartment of Paediatrics, Region Jönköping County, Jönköping, SwedenDepartment of Biomedical and Clinical Sciences, Linköping University, Linköping, SwedenLaboratory Medicine, Region Jönköping County, Jönköping, SwedenIntroduction 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.https://bmjopengastro.bmj.com/content/7/1/e000536.full |
| spellingShingle | Mats Fredrikson Hanna Gustafsson Bragde Ulf Jansson Ewa Grodzinsky Jan Söderman Characterisation of gene and pathway expression in stabilised blood from children with coeliac disease BMJ Open Gastroenterology |
| title | Characterisation of gene and pathway expression in stabilised blood from children with coeliac disease |
| title_full | Characterisation of gene and pathway expression in stabilised blood from children with coeliac disease |
| title_fullStr | Characterisation of gene and pathway expression in stabilised blood from children with coeliac disease |
| title_full_unstemmed | Characterisation of gene and pathway expression in stabilised blood from children with coeliac disease |
| title_short | Characterisation of gene and pathway expression in stabilised blood from children with coeliac disease |
| title_sort | characterisation of gene and pathway expression in stabilised blood from children with coeliac disease |
| url | https://bmjopengastro.bmj.com/content/7/1/e000536.full |
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