Identification of master regulators in goblet cells and Paneth cells using transcriptomics profiling of gut organoids and multi-layered networks

Dysfunction of intestinal epithelial cells is often associated with severe gut pathologies, such as inflammatory bowel disease (IBD). Although transcriptional signatures of intestinal cells have been identified, an integrated network analysis of specific cell types which identifies key regulators and disease relevance has been lacking. Here, we profiled the expression of mRNAs, microRNAs and long non-coding RNAs from mouse derived 3D intestinal organoids whose differentiation was directed towards Paneth cells or goblet cells. We generated regulatory networks specific to these cell types by integrating expression data into networks of transcriptional and post-transcriptional regulatory interactions. Analysis of the networks uncovered potential cell-type specific master regulators and highlighted possible regulatory rewiring between the cell types. Investigation of regulators identified links to cellular phenotypes associated with IBD. Application of our workflow can be used to disentangle multifactorial mechanisms of IBD and to propose regulators whose pharmacological targeting could be advantageous in treating Crohn’s disease.

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Author Treveil, A
Last Updated November 20, 2019, 16:45 (UTC)
Created August 1, 2019, 10:27 (UTC)
Article Host Type publisher
Article Is Open Access true
Article License Type cc-by
Article Version Type publishedVersion
Citation Report https://scite.ai/reports/10.1101/575845
DOI 10.1101/575845
Date Last Updated 2019-06-27T04:43:58.173821
Evidence open (via page says license)
Funder code(s)
Journal Is Open Access false
Open Access Status hybrid
PDF URL https://www.biorxiv.org/content/biorxiv/early/2019/05/01/575845.full.pdf
Publisher URL https://doi.org/10.1101/575845