A systems biology approach to investigate cell fate switches in intestinal organoids

Project Information

SysOrganoid

Grant agreement ID: 771059

DOI 10.3030/771059

Project closed

EC signature date 6 February 2018

Start date 1 October 2018

End date 30 September 2023

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost € 2 000 000,00

EU contribution € 2 000 000,00

Coordinated by

STICHTING RADBOUD UNIVERSITEIT
Netherlands

Publications

Peer reviewed articles (10)

Retinoic acid signaling drives differentiation toward the absorptive lineage in colorectal cancer

Author(s): Roelof A. Wester, Lisa van Voorthuijsen, Hannah K. Neikes, Jelmer J. Dijkstra, Lieke A. Lamers, Siebren Frölich, Maarten van der Sande, Colin Logie, Rik G.H. Lindeboom, Michiel Vermeulen
Published in: iScience, Issue 24/12, 2021, Page(s) 103444, ISSN 2589-0042
Publisher: Cell Press
DOI: 10.1016/j.isci.2021.103444

RNF 43 truncations trap CK 1 to drive niche‐independent self‐renewal in cancer

Author(s): Maureen Spit, Nicola Fenderico, Ingrid Jordens, Tomasz Radaszkiewicz, Rik GH Lindeboom, Jeroen M Bugter, Alba Cristobal, Lars Ootes, Max van Osch, Eline Janssen, Kim E Boonekamp, Katerina Hanakova, David Potesil, Zbynek Zdrahal, Sylvia F Boj, Jan Paul Medema, Vitezslav Bryja, Bon‐Kyoung Koo, Michiel Vermeulen, Madelon M Maurice
Published in: The EMBO Journal, Issue 39/18, 2020, ISSN 0261-4189
Publisher: Nature Publishing Group
DOI: 10.15252/embj.2019103932

Off-the-shelf proximity biotinylation for interaction proteomics

Author(s): Irene Santos-Barriopedro, Guido van Mierlo, Michiel Vermeulen
Published in: Nature Communications, Issue 12/1, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-25338-4

Probing the Tumor Suppressor Function of BAP1 in CRISPR-Engineered Human Liver Organoids

Author(s): Benedetta Artegiani, Lisa van Voorthuijsen, Rik G.H. Lindeboom, Daniëlle Seinstra, Inha Heo, Pablo Tapia, Carmen López-Iglesias, Daniel Postrach, Talya Dayton, Rurika Oka, Huili Hu, Ruben van Boxtel, Johan H. van Es, Johan Offerhaus, Peter J. Peters, Jacco van Rheenen, Michiel Vermeulen, Hans Clevers
Published in: Cell Stem Cell, Issue 24/6, 2019, Page(s) 927-943.e6, ISSN 1934-5909
Publisher: Cell Press
DOI: 10.1016/j.stem.2019.04.017

ONECUT2 regulates RANKL-dependent enterocyte and microfold cell differentiation in the small intestine; a multi-omics study

Author(s): Maria V Luna Velez; Hannah K Neikes; Rebecca R Snabel; Yarah Quint; Chen Qian; Aniek Martens; Gert Jan C Veenstra; Michael R Freeman; Simon J van Heeringen; Michiel Vermeulen
Published in: Nucleic Acids Research, Issue 51 (3), 2023, Page(s) 1277–1296, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkac1236

Multiomics of Colorectal Cancer Organoids Reveals Putative Mediators of Cancer Progression Resulting from SMAD4 Inactivation.

Author(s): Jelmer J. Dijkstra; Hannah K. Neikes; Somayeh Rezaeifard; Xuhui Ma; Emile E. Voest; Daniele V. F. Tauriello; Michiel Vermeulen
Published in: J. Proteome Res., Issue 22, 2022, Page(s) 138–151, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.2c00551

Miniaturised interaction proteomics on a microfluidic platform with ultra-low input requirements

Author(s): Cristina Furlan, René A. M. Dirks, Peter C. Thomas, Robert C. Jones, Jing Wang, Mark Lynch, Hendrik Marks, Michiel Vermeulen
Published in: Nature Communications, Issue 10/1, 2019, Page(s) 1525, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-019-09533-y

Determining DNA–Protein Binding Affinities and Specificities from Crude Lysates Using a Combined SILAC/TMT Labeling Strategy

Author(s): Cathrin Gräwe; Miguel Hernandez-Quiles; Pascal W. T. C. Jansen; Annika Brimmers; Michiel Vermeulen
Published in: J. Proteome Res, Issue 22 (8), 2023, Page(s) 2683-2693, ISSN 1535-3893
Publisher: American Chemical Society
DOI: 10.1021/acs.jproteome.3c00248

STPP-UP: An alternative method for drug target identification using protein thermal stability

Author(s): Dick W. Zijlmans; Miguel Hernández-Quiles; Pascal W.T.C. Jansen; Isabelle Becher; Frank Stein; Mikhail M. Savitski; Michiel Vermeulen
Published in: J Biol Chem, Issue 299 (11), 2023, Page(s) 105279, ISSN 0021-9258
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.jbc.2023.105279

Quantification of absolute transcription factor binding affinities in the native chromatin context using BANC-seq

Author(s): Hannah K. Neikes, Katarzyna W. Kliza, Cathrin Gräwe, Roelof A. Wester, Pascal W. T. C. Jansen, Lieke A. Lamers, Marijke P. Baltissen, Simon J. van Heeringen, Colin Logie, Sarah A. Teichmann, Rik G. H. Lindeboom & Michiel Vermeulen
Published in: Nature Biotechnology, 2023, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.1038/s41587-023-01715-w