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Cell Stem Cell. 2019 Jun 6;24(6):927-943.e6. doi: 10.1016/j.stem.2019.04.017. Epub 2019 May 23.

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

Author information

1
Oncode Institute, Utrecht, the Netherlands; Hubrecht Institute, KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht, the Netherlands.
2
Oncode Institute, Utrecht, the Netherlands; Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Science, Radboud University Nijmegen, Nijmegen, the Netherlands.
3
Oncode Institute, Utrecht, the Netherlands; Molecular Pathology, the Netherlands Cancer Institute, Amsterdam, the Netherlands.
4
Hubrecht Institute, KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht, the Netherlands.
5
The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, 6229ER Maastricht, the Netherlands.
6
The Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands.
7
Oncode Institute, Utrecht, the Netherlands; The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Genetics, School of Basic Medical Sciences, Shandong University, 250012 Jinan, China.
8
Department of Pathology, UMC Utrecht, 3584CX Utrecht, the Netherlands.
9
Oncode Institute, Utrecht, the Netherlands; Hubrecht Institute, KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht, the Netherlands; The Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands; University Medical Center Utrecht, Cancer Genomics Netherlands, 3584CX Utrecht, the Netherlands. Electronic address: h.clevers@hubrecht.eu.

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:

BAP1; CRISPR/Cas9; cancer; cholangiocarcinoma; epigenetics; genome editing; human organoids; liver; tumor modeling

PMID:
31130514
DOI:
10.1016/j.stem.2019.04.017

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