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Cambridge Immunology Network



Our research theme is focused on epigenetics of the intestinal immune system in health and disease particularly inflammatory bowel disease (IBD). Specifically, we are currently exploring the impact of epigenetic mechanisms such as DNA methylation and histone modifications on regulating gene expression of the human intestinal epithelium. We are taking a systems biology approach by applying genome wide molecular profiling of primary tissue and patient derived organoid cultures in order to elucidate pathophysiological mechanisms implicated in gut health and disease. Our aim is to translate findings form bench to the bedside in order to
improve life of children suffering from GI disorders.


Key publications: 

1.            Kraiczy J, Zilbauer M. Intestinal Epithelial Organoids as Tools to Study Epigenetics in Gut Health and Disease. Stem Cells Int 2019;2019:7242415.

2.            Kraiczy J, Ross ADB, Forbester JL, Dougan G, Vallier L, Zilbauer M. Genome-Wide Epigenetic and Transcriptomic Characterization of Human-Induced Pluripotent Stem Cell-Derived Intestinal Epithelial Organoids. Cell Mol Gastroenterol Hepatol 2019;7:285-288.

3.            Kraiczy J, Nayak KM, Howell KJ, Ross A, Forbester J, Salvestrini C, Mustata R, Perkins S, Andersson-Rolf A, Leenen E, Liebert A, Vallier L, Rosenstiel PC, Stegle O, Dougan G, Heuschkel R, Koo BK, Zilbauer M. DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development. Gut 2019;68:49-61.

4.            Jung KB, Lee H, Son YS, Lee MO, Kim YD, Oh SJ, Kwon O, Cho S, Cho HS, Kim DS, Oh JH, Zilbauer M, Min JK, Jung CR, Kim J, Son MY. Interleukin-2 induces the in vitro maturation of human pluripotent stem cell-derived intestinal organoids. Nat Commun 2018;9:3039.

5.            Howell KJ, Kraiczy J, Nayak KM, Gasparetto M, Ross A, Lee C, Mak TN, Koo BK, Kumar N, Lawley T, Sinha A, Rosenstiel P, Heuschkel R, Stegle O, Zilbauer M. DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome. Gastroenterology 2018;154:585-598.

6.            Kraiczy J, Nayak K, Ross A, Raine T, Mak TN, Gasparetto M, Cario E, Rakyan V, Heuschkel R, Zilbauer M. Assessing DNA methylation in the developing human intestinal epithelium: potential link to inflammatory bowel disease. Mucosal Immunol 2016;9:647-58.

7.            Zilbauer M, Rayner TF, Clark C, Coffey AJ, Joyce CJ, Palta P, Palotie A, Lyons PA, Smith KG. Genome-wide methylation analyses of primary human leukocyte subsets identifies functionally important cell-type-specific hypomethylated regions. Blood 2013;122:e52-60.

Dr Matthias  Zilbauer
Takes PhD students
Available for consultancy


Departments and institutes: 
Person keywords: 
Human gut organoids
Mucosal immunology
DNA methylation
Intestinal epithelial cell biology