How do intercellular interactions differ in Ulcerative colitis compared to healthy gut?

Mentors: Dezso Modos and Marton Olbei

Overview

Ulcerative colitis is an inflammatory bowel disease. The exact pathomechanism of the disease is unknown. However, the interactions between the intestinal immune cells and the intestinal epithelial cells play a crucial role during the development of the disease. Single-cell RNA-seq measurements can help us understand these complex interactions. The expression data combined with protein-protein interaction databases can shed light on the connections between cells in diseased and healthy states.

During this project trainees will use the Smilie et al single-cell RNA-seq data to build interactions between the various cells. The data set contain pre-processed, cell type classified data of biopsies from healthy, inflamed and non-inflamed UC colonic biopsies. The interactions between cells will be downloaded from the OmniPath database. Students will need to use python notebooks to build up the intercellular networks, map the single cell RNA-seq expression data and then visualise them. The intercellular networks between various cell types can be compared by Cytoscape using the DyNet plugin.

Training materials:

• Presentation slides
• Practical materials including scripts

Suggested reading:

• Smillie CS, Biton M, Ordovas-Montanes J, Sullivan KM, Burgin G, Graham DB, et al. Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis. Cell. 2019 Jul 25;178(3):714–730.e22.
• Türei D, Korcsmáros T, Saez-Rodriguez J. OmniPath: guidelines and gateway for literature-curated signaling pathway resources. Nat Methods. 2016 Nov 29;13(12):966–967.
• Goenawan IH, Bryan K, Lynn DJ. DyNet: visualization and analysis of dynamic molecular interaction networks. Bioinformatics. 2016 Sep 1;32(17):2713-5.