Research Article: RNA sequencing of intestinal mucosa reveals novel pathways functionally linked to celiac disease pathogenesis

Date Published: April 18, 2019

Publisher: Public Library of Science

Author(s): Maureen M. Leonard, Yu Bai, Gloria Serena, Kourtney P. Nickerson, Stephanie Camhi, Craig Sturgeon, Shu Yan, Maria R. Fiorentino, Aubrey Katz, Barbara Nath, James Richter, Matthew Sleeman, Cagan Gurer, Alessio Fasano, Karol Sestak.

http://doi.org/10.1371/journal.pone.0215132

Abstract

The early steps in the pathophysiology of celiac disease (CD) leading to loss of tolerance to gluten are poorly described. Our aim was to use RNA sequencing of duodenal biopsies in patients with active CD, CD in remission, and non-CD controls to gain insight into CD pathophysiology, identify additional genetic signatures linked to CD, and possibly uncover targets for future therapeutic agents.

We performed whole transcriptome shotgun sequencing of intestinal biopsies in subjects with active and remission CD and non-CD controls. We also performed functional pathway analysis of differentially expressed genes to identify statistically significant pathways that are up or down regulated in subjects with active CD compared to remission CD.

We identified the upregulation of novel genes including IL12R, ITGAM and IGSF4 involved in the immune response machinery and cell adhesion process in the mucosa of subjects with active CD compared to those in remission. We identified a unique signature of genes, related to innate immunity, perturbed exclusively in CD irrespective of disease status. Finally, we highlight novel pathways of interest that may contribute to the early steps of CD pathogenesis and its comorbidities such as the spliceosome, pathways related to the innate immune response, and pathways related to autoimmunity.

Our study confirmed previous findings based on GWAS and immunological studies pertinent to CD pathogenesis and describes novel genes and pathways that with further validation may be found to contribute to the early steps in the pathogenesis of CD, ongoing inflammation, and comorbidities associated with CD.

Partial Text

Celiac disease (CD) is a chronic systemic autoimmune disease that occurs globally in genetically predisposed individuals in response to ingestion of gluten-containing grains[1]. While the pathognomonic damage occurs in the small intestine, clinical manifestations are varied and include both intestinal and extra-intestinal symptoms[2]. CD is a unique autoimmune disease in that there is a strong genetic component, notably human leukocyte antigen (HLA) DQ2 and DQ8[3]. During active disease, the production of autoantibodies against tissue transglutaminase (anti-tTG2) can be measured in the blood to indicate the presence of disease. While HLA DQ2 and/or DQ8 and gluten ingestion are necessary to develop CD, they are not sufficient as most individuals with compatible HLA do not develop CD. Furthermore, CD can develop at any age[4] but what leads ultimately to this loss of tolerance to gluten and development of intestinal inflammation is unknown.

Our analysis of subjects with active CD compared to those in remission and non-CD controls using whole transcriptome shotgun sequencing of duodenal biopsies revealed results consistent with many of the previously described pathways identified in the pathogenesis of CD, suggesting that our analysis is robust. Our finding that patients with CD, irrespective of disease status, have a constitutive upregulation of pathways related to innate immunity confirms the important role of the innate immune system in CD pathogenesis. By focusing on the statistically significant pathways that are up or down regulated in subjects with active CD compared to those in remission, we identified novel pathways of interest such as the spliceosome pathway that may contribute to the early steps involved in losing tolerance to gluten. We also identified novel genes involved in the immune response machinery (IL-12RB1and IL-12RB2) and cell adhesion process (IGSF4 and ITGAM) in the mucosa of subjects with active CD compared to those in remission. Together, our findings support a possible link between the microbiome, innate immune response, and the development of CD and highlight possible associations that with future validation may lead to crucial knowledge of the steps leading to loss of tolerance to gluten. Finally, we also suggest possible molecular mechanisms for the association with other autoimmune diseases and persistent enteropathy despite a strict gluten free diet. Our data serve to act as a launching point to suggest areas of further investigation and validation for CD pathogenesis, treatment, and associations with other autoimmune disease.

 

Source:

http://doi.org/10.1371/journal.pone.0215132

 

Leave a Reply

Your email address will not be published.