@article{39a135cb37ae4e3ab1edbc53f577699b,
title = "Probing the Tumor Suppressor Function of BAP1 in CRISPR-Engineered Human Liver Organoids",
abstract = "The deubiquitinating enzyme BAP1 is a tumor suppressor, among others involved in cholangiocarcinoma. BAP1 has many proposed molecular targets, while its Drosophila homolog is known to deubiquitinate histone H2AK119. We introduce BAP1 loss-of-function by CRISPR/Cas9 in normal human cholangiocyte organoids. We find that BAP1 controls the expression of junctional and cytoskeleton components by regulating chromatin accessibility. Consequently, we observe loss of multiple epithelial characteristics while motility increases. Importantly, restoring the catalytic activity of BAP1 in the nucleus rescues these cellular and molecular changes. We engineer human liver organoids to combine four common cholangiocarcinoma mutations (TP53, PTEN, SMAD4, and NF1). In this genetic background, BAP1 loss results in acquisition of malignant features upon xenotransplantation. Thus, control of epithelial identity through the regulation of chromatin accessibility appears to be a key aspect of BAP1's tumor suppressor function. Organoid technology combined with CRISPR/Cas9 provides an experimental platform for mechanistic studies of cancer gene function in a human context.",
keywords = "STEM-CELL ORGANOIDS, INTRAHEPATIC CHOLANGIOCARCINOMA, WHOLE-GENOME, MUTATIONS, EXPRESSION, MODELS, FRACTIONATION, INFECTION, CHROMATIN, PROTEINS",
author = "Benedetta Artegiani and {van Voorthuijsen}, Lisa and Lindeboom, {Rik G. H.} and Danielle Seinstra and Inha Heo and Pablo Tapia and Carmen Lopez-Iglesias and Daniel Postrach and Talya Dayton and Rurika Oka and Huili Hu and {van Boxtel}, Ruben and {van Es}, {Johan H.} and Johan Offerhaus and Peters, {Peter J.} and {van Rheenen}, Jacco and Michiel Vermeulen and Hans Clevers",
note = "Funding Information: We thank Jeroen Korving and Harry Begthel for help with histology, Stieneke van den Brink for support with media components, and the Microscopy Core Lab (M4I Maastricht University) components for their help in TEM. The authors wish to thank Oded Kopper for discussion and Carmine Ortix for help with figure preparation. We acknowledge all the anonymous liver tissue donors. J.v.R. thanks the Josef Steiner Cancer Research Foundation for funding. This work is part of the Oncode Institute that is partly financed by the Dutch Cancer Society and was funded by the gravitation program CancerGenomiCs.nl from the Netherlands Organization for Scientific Research (NWO), MKMD ( 114021012 ) from NWO-ZonMw , and from Stichting Vrienden van Hubrecht 2012.10 . B.A. was supported by a FEBS Long-term fellowship and is the recipient of a VENI grant ( NWO-ALW 863.15.015 ). I.H. is the recipient of a VENI grant ( NWO-ALW 863.14.002 ). T.D. was supported by an EMBO fellowship. The Vermeulen lab is supported by an ERC Consolidator Grant (SysOrganoid; 771059 ). Funding Information: We thank Jeroen Korving and Harry Begthel for help with histology, Stieneke van den Brink for support with media components, and the Microscopy Core Lab (M4I Maastricht University) components for their help in TEM. The authors wish to thank Oded Kopper for discussion and Carmine Ortix for help with figure preparation. We acknowledge all the anonymous liver tissue donors. J.v.R. thanks the Josef Steiner Cancer Research Foundation for funding. This work is part of the Oncode Institute that is partly financed by the Dutch Cancer Society and was funded by the gravitation program CancerGenomiCs.nl from the Netherlands Organization for Scientific Research (NWO), MKMD (114021012) from NWO-ZonMw, and from Stichting Vrienden van Hubrecht 2012.10. B.A. was supported by a FEBS Long-term fellowship and is the recipient of a VENI grant (NWO-ALW 863.15.015). I.H. is the recipient of a VENI grant (NWO-ALW 863.14.002). T.D. was supported by an EMBO fellowship. The Vermeulen lab is supported by an ERC Consolidator Grant (SysOrganoid; 771059). Conceptualization, B.A. and H.C.; Methodology, B.A. M.V. and H.C.; Software, B.A. and R.L.; Formal Analysis, B.A. and R.L.; Investigation, B.A. L.v.V. I.H. D.S. P.T. C.L.-I. D.P. and T.D.; Resources, B.A. H.H. J.O. J.H.v.E. and J.v.R.; Data Curation, B.A. L.v.V. and R.L.; Writing – Original Draft, B.A. and H.C.; Writing – Review & Editing, B.A. H.C. T.D. J.O. L.v.V. and R.L.; Visualization, B.A. and R.L.; Supervision, J.v.R. M.V. and H.C.; Project Administration, B.A. and H.C.; Funding Acquisition, B.A. P.J.P. J.v.R. M.V. and H.C. H.C. holds several patents on organoid technology. Their application numbers, followed by their publication numbers (if applicable), are as follows; PCT/NL2008/050543, WO2009/022907; PCT/NL2010/000017, WO2010/090513; PCT/IB2011/002167, WO2012/014076; PCT/IB2012/052950, WO2012/168930; PCT/EP2015/060815, WO2015/173425; PCT/EP2015/077990, WO2016/083613; PCT/EP2015/077988, WO2016/083612; PCT/EP2017/054797, WO2017/149025; PCT/EP2017/065101, WO2017/220586; PCT/EP2018/086716, n/a; and GB1819224.5, n/a. Publisher Copyright: {\textcopyright} 2019 Elsevier Inc.",
year = "2019",
month = jun,
day = "6",
doi = "10.1016/j.stem.2019.04.017",
language = "English",
volume = "24",
pages = "927--943.e6",
journal = "Cell Stem Cell",
issn = "1934-5909",
publisher = "Cell Press",
number = "6",
}