@article{663fd8f8b28c41998709f3aaef6b54c4,
title = "Genome-Scale CRISPR Screening in Human Intestinal Organoids Identifies Drivers of TGF-β Resistance",
abstract = "Forward genetic screens with genome-wide CRISPR libraries are powerful tools for resolving cellular circuits and signaling pathways. Applying this technology to organoids, however, has been hampered by technical limitations. Here we report improved accuracy and robustness for pooled-library CRISPR screens by capturing sgRNA integrations in single organoids, substantially reducing required cell numbers for genome-scale screening. We applied our approach to wild-type and APC mutant human intestinal organoids to identify genes involved in resistance to TGF-β-mediated growth restriction, a key process during colorectal cancer progression, and validated hits including multiple subunits of the tumor-suppressive SWI/SNF chromatin remodeling complex. Mutations within these genes require concurrent inactivation of APC to promote TGF-β resistance and attenuate TGF-β target gene transcription. Our approach can be applied to a variety of assays and organoid types to facilitate biological discovery in primary 3D tissue models.",
keywords = "APC, ATAC, colorectal cancer, CRISPR screen, Cut and Run, organoids, SWI/SNF, TGFb",
author = "Till Ringel and Nina Frey and Femke Ringnalda and Sharan Janjuha and Sarah Cherkaoui and Stefan Butz and Sumana Srivatsa and Martin Pirkl and Giancarlo Russo and Lukas Villiger and Gerhard Rogler and Hans Clevers and Niko Beerenwinkel and Nicola Zamboni and Tuncay Baubec and Gerald Schwank",
note = "Funding Information: We thank J. Huotari, S. Ringer, M. Jovanovic, and T. Beyer for discussions and input on the manuscript; J. Schueler and D. Lenhard for their help with performing transplantation experiments; and K. Meier and N. Gampp for their experimental support. This work was funded by the SNSF ( 160230 ). T.R. holds a PhD scholarship from ETH Zurich. L.V. holds an MD/PhD scholarship from the SNSF. Funding Information: We thank J. Huotari, S. Ringer, M. Jovanovic, and T. Beyer for discussions and input on the manuscript; J. Schueler and D. Lenhard for their help with performing transplantation experiments; and K. Meier and N. Gampp for their experimental support. This work was funded by the SNSF (160230). T.R. holds a PhD scholarship from ETH Zurich. L.V. holds an MD/PhD scholarship from the SNSF. Conceptualization, T.R. and G.S.; Methodology, T.R. N.F. and G.S.; Software, S.C.; Formal Analysis, S.J. N.F. S.C. S.S. M.P. N.B. T.B. S.B. and G. Russo; Investigation, T.R. N.F. F.R. S.B. and L.V.; Resources, G. Rogler and H.C.; Data Curation, T.R. S.J. and G. Russo; Writing ? Original Draft, T.R. and G.S.; Writing ? Review & Editing, T.R. G.S. N.F. and S.J.; Project Administration, T.R. and G.S. H.C. is an inventor on applications/patents related to organoid technology. The other authors declare no competing interests. Publisher Copyright: {\textcopyright} 2020 Elsevier Inc. Copyright: Copyright 2020 Elsevier B.V., All rights reserved.",
year = "2020",
month = mar,
day = "5",
doi = "10.1016/j.stem.2020.02.007",
language = "English",
volume = "26",
pages = "431--440.e8",
journal = "Cell stem cell",
issn = "1934-5909",
publisher = "Cell Press",
number = "3",
}