New project starting October 2018 => more information
Maintaining the structure of the intestinal microbiota is a major task of the intestinal epithelium, which serves as the primary interface between the (microbial) environment and the host. A large body of evidence has been put forward that disturbed host-microbial interactions and related inflammatory signaling play an important role in the etiology of a number of chronic inflammatory disorders affecting barrier organs (e.g. inflammatory bowel diseases, psoriasis), but also in metabolic diseases (obesity, type 2 diabetes) and certain forms of cancer affecting the gastrointestinal tract (e.g. colonic or hepatocellular cancer).
The intestinal epithelium is a rapidly renewing tissue comprising several cell types with differential turnover rates and differentiation patterns: Enterocytes sensu strictu, goblet cells, Paneth cells (mostly found in the ileum) and neuroendocrine cells. The role of de novo methylation for fine tuning of this process has been postulated however so far only little functional evidence has been presented and some controversies remain. DNMT3A/B are important enzymes of de novo methylation and genetic variants in human DNMT3A and -B loci have been associated with an increased risk of inflammatory bowel disease (Franke, 2010 and Jostins, 2012). A recent study has shown that inactivation of DNMT3A in intestinal epithelial cells is linked to protection against hereditary CRC in the Apc/Min+ model. In contrast, somatic inactivating mutations are recurrently found in acute myeloid leukemia, which would argue for a tumor suppressor role of the gene. In IBD, the role of the associated variants of DNMT3A/B is not fully understood: a small study identified no association of global mucosal methylation patterns between the allelic variants of DNMT3A (Nimmo, 2012)and, an upregulation of the DNMT3B transcript in the IBD mucosa has been suggested. We have shown previously that several loci in the diseased mucosa are differentially methylated in monozygotic discordant twins (Haesler et al, 2012).
We hypothesize that DNMT3A and B may play an important role in maintaining stability of DNA methylation patterns in IECs under physiological conditions. Thus, their genetic dysregulation might be involved in initiation and perpetuation of inflammation in IBD as well as inflammation-associated carcinogenesis in the gut.
The selected doctoral researcher will work on the following major topics:
- to assess the functional consequences of DNMT3A/B deletion for intestinal epithelial self renewal and lineage decisions in vitro and in vivo
- to build a genome-wide map of the DNA methylation marks in DNMT3A WT and conditional KO animals
- to test the functional relevance of DNMT3A/B and/or chemical methylation inhibitors in models of intestinal inflammation and inflammation-associated carcinogenesis and demonstrate the potential involvement of the gut-associated microbial homeostasis
The doctoral researcher will use DNA methylation/RNA analysis as well as animal models of IBD and perform wet lab work around organoid cultures. The outlined experiments include the generation of high-throughput data sets as a hypothesis generation for selection of candidates and functional follow-up, but not as a mere catalogue of epigenetic marks. As described before, independent validation experiments will be performed on selected candidates to technically verify the NGS data sets.
The project thus requires analytical skills both in the wet lab as well as on the computational side. It is expected that the doctoral researcher has either thorough knowledge of molecular biology/genomics techniques or profound computational skills at the outset. Over the course of the project, the PI/Co-PI team will guarantee a well-balanced education to complement the analytical skills for the planned analyses.
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4: Hashimoto T, Perlot T, Rehman A, Trichereau J, Ishiguro H, Paolino M, Sigl V, Hanada T, Hanada R, Lipinski S, Wild B, Camargo SM, Singer D, Richter A, Kuba K, Fukamizu A, Schreiber S, Clevers H, Verrey F, Rosenstiel P*, Penninger JM. ACE2links amino acid malnutrition to microbial ecology and intestinal inflammation. Nature. 2012 Jul 25;487(7408):477-81. doi: 10.1038/nature11228. PubMed PMID:22837003.
5: Häsler R, Feng Z, Bäckdahl L, Spehlmann ME, Franke A, Teschendorff A, Rakyan VK, Down TA, Wilson GA, Feber A, Beck S, Schreiber S, Rosenstiel P. A functional methylome map of ulcerative colitis. Genome Res. 2012 Nov;22(11):2130-7. doi:10.1101/gr.138347.112. Epub 2012 Jul 23. PubMed PMID: 22826509; PubMed CentralPMCID: PMC3483542.