Uncoupling of mucosal gene regulation, mRNA splicing and adherent microbiota signatures in inflammatory bowel disease

Research output: Contribution to journalArticle

  • External authors:
  • Robert Häsler
  • Raheleh Sheibani-Tezerji
  • Anupam Sinha
  • Matthias Barann
  • Ateequr Rehman
  • Daniela Esser
  • Konrad Aden
  • Carolin Knecht
  • Berenice Brandt
  • Susanna Nikolaus
  • Sascha Schäuble
  • Christoph Kaleta
  • Andre Franke
  • Christoph Fretter
  • Marc-Thorsten Hütt
  • Michael Krawczak
  • Stefan Schreiber
  • Philip Rosenstiel


Objective An inadequate host response to the intestinal microbiota likely contributes to the manifestation and progression of human inflammatory bowel disease (IBD). However, molecular approaches to unravelling the nature of the defective crosstalk and its consequences for intestinal metabolic and immunological networks are lacking. We assessed the mucosal transcript levels, splicing architecture and mucosa-attached microbial communities of patients with IBD to obtain a comprehensive view of the underlying, hitherto poorly characterised interactions, and how these are altered in IBD.

Design Mucosal biopsies from Crohn's disease and patients with UC, disease controls and healthy individuals (n=63) were subjected to microbiome, transcriptome and splicing analysis, employing next-generation sequencing. The three data levels were integrated by different bioinformatic approaches, including systems biology-inspired network and pathway analysis.

Results Microbiota, host transcript levels and host splicing patterns were influenced most strongly by tissue differences, followed by the effect of inflammation. Both factors point towards a substantial disease-related alteration of metabolic processes. We also observed a strong enrichment of splicing events in inflamed tissues, accompanied by an alteration of the mucosa-attached bacterial taxa. Finally, we noted a striking uncoupling of the three molecular entities when moving from healthy individuals via disease controls to patients with IBD.

Conclusions Our results provide strong evidence that the interplay between microbiome and host transcriptome, which normally characterises a state of intestinal homeostasis, is drastically perturbed in Crohn's disease and UC. Consequently, integrating multiple OMICs levels appears to be a promising approach to further disentangle the complexity of IBD.

Bibliographical metadata

Original languageEnglish
Number of pages11
Early online date30 Sep 2016
Publication statusPublished - 2016