Zilbauer Lab

About

Welcome to the Zilbauer Lab at the University of Cambridge. We are a multidisciplinary team passionate about understanding the human intestinal epithelium, with a particular focus on paediatric inflammatory bowel diseases. By combining clinical insight with cutting-edge science, our research explores how epigenetic mechanisms—especially DNA methylation—regulate intestinal epithelial stem cell function during development, homeostasis, and disease. Using a unique biobank of hundreds of patient-derived intestinal organoids, we model the gut epithelium in a patient-specific manner to uncover how molecular changes contribute to disease pathogenesis, severity, and treatment response. Our work integrates state-of-the-art technologies including single-cell sequencing and CRISPR screening, with the ultimate goal of translating findings into personalized therapies for children. We welcome collaborations and new trainees who are excited to push boundaries in gut epithelium research and translational epigenetics.

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Key publications

• Patient-derived organoid biobank identifies epigenetic dysregulation of intestinal epithelial MHC-I as a novel mechanism in severe Crohn's Disease

Dennison TW, Edgar RD, Payne F, Nayak KM, Ross ADB, Cenier A, Glemas C, Giachero F, Foster AR, Harris R, Kraiczy J, Salvestrini C, Stavrou G, Torrente F, Brook K, Trayers C, Elmentaite R, Youssef G, Tél B, Winton DJ, Skoufou-Papoutsaki N, Adler S, Bufler P, Azabdaftari A, Jenke A, G N, Thomas N, Miele E, Al-Mohammad A, Guarda G, Kugathasan S, Venkateswaran S, Clatworthy MR, Castro-Dopico T, Suchanek O, Strisciuglio C, Gasparetto M, Lee S, Xu X, Bello E, Han N, Zerbino DR, Teichmann SA, Nys J, Heuschkel R, Perrone F, Zilbauer M. Patient-derived organoid biobank identifies epigenetic dysregulation of intestinal epithelial MHC-I as a novel mechanism in severe Crohn's Disease. Gut. 2024 Aug 8;73(9):1464-1477. doi: 10.1136/gutjnl-2024-332043. PMID: 38857990; PMCID: PMC11347221.

• Culture-Associated DNA Methylation Changes Impact on Cellular Function of Human Intestinal Organoids.

Edgar RD, Perrone F, Foster AR, Payne F, Lewis S, Nayak KM, Kraiczy J, Cenier A, Torrente F, Salvestrini C, Heuschkel R, Hensel KO, Harris R, Jones DL, Zerbino DR, Zilbauer M. Cell Mol Gastroenterol Hepatol. 2022;14(6):1295-1310. doi: 10.1016/j.jcmgh.2022.08.008. Epub 2022 Aug 28.

• Single-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn's Disease.

Elmentaite R, Ross ADB, Roberts K, James KR, Ortmann D, Gomes T, Nayak K, Tuck L, Pritchard S, Bayraktar OA, Heuschkel R, Vallier L, Teichmann SA, Zilbauer M.Dev Cell. 2020 Dec 21;55(6):771-783.e5. doi: 10.1016/j.devcel.2020.11.010. Epub 2020 Dec 7.

• DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development.

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. Gut. 2019 Jan;68(1):49-61. doi: 10.1136/gutjnl-2017-314817. Epub 2017 Nov 15

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