Identification and characterization of essential genes in the human genome
Timothy C. Wang,Kıvanç Birsoy,Nicholas W. Hughes,Kevin M. Krupczak,Yorick Post,Yorick Post,Jenny J. Wei,Eric S. Lander,Eric S. Lander,Eric S. Lander,David M. Sabatini +10 more
TLDR
Using the bacterial clustered regularly interspaced short palindromic repeats (CRISPR) system, this article constructed a genome-wide single-guide RNA library to screen for genes required for proliferation and survival in a human cancer cell line.Abstract:
Large-scale genetic analysis of lethal phenotypes has elucidated the molecular underpinnings of many biological processes. Using the bacterial clustered regularly interspaced short palindromic repeats (CRISPR) system, we constructed a genome-wide single-guide RNA library to screen for genes required for proliferation and survival in a human cancer cell line. Our screen revealed the set of cell-essential genes, which was validated with an orthogonal gene-trap-based screen and comparison with yeast gene knockouts. This set is enriched for genes that encode components of fundamental pathways, are expressed at high levels, and contain few inactivating polymorphisms in the human population. We also uncovered a large group of uncharacterized genes involved in RNA processing, a number of whose products localize to the nucleolus. Last, screens in additional cell lines showed a high degree of overlap in gene essentiality but also revealed differences specific to each cell line and cancer type that reflect the developmental origin, oncogenic drivers, paralogous gene expression pattern, and chromosomal structure of each line. These results demonstrate the power of CRISPR-based screens and suggest a general strategy for identifying liabilities in cancer cells.read more
Citations
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Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9
John G. Doench,Nicolo Fusi,Meagan E Sullender,Mudra Hegde,Emma W Vaimberg,Katherine F Donovan,Ian Smith,Zuzana Tothova,Zuzana Tothova,Craig B. Wilen,Robert C. Orchard,Herbert W. Virgin,Jennifer Listgarten,David E. Root +13 more
TL;DR: Recently devised sgRNA design rules are used to create human and mouse genome-wide libraries, perform positive and negative selection screens and observe that the use of these rules produced improved results, and a metric to predict off-target sites is developed.
Journal ArticleDOI
Defining a Cancer Dependency Map
Aviad Tsherniak,Francisca Vazquez,Francisca Vazquez,Phil Montgomery,Barbara A. Weir,Barbara A. Weir,Gregory Kryukov,Gregory Kryukov,Glenn S. Cowley,Stanley Gill,Stanley Gill,William F. Harrington,Sasha Pantel,John M. Krill-Burger,Robin M. Meyers,Levi D. Ali,Amy Goodale,Yenarae Lee,Guozhi Jiang,Jessica Hsiao,William F.J Gerath,Sara Howell,Erin Merkel,Mahmoud Ghandi,Levi A. Garraway,David E. Root,Todd R. Golub,Jesse S. Boehm,William C. Hahn +28 more
TL;DR: DEMETER, an analytical framework that segregates on- from off-target effects of RNAi, demonstrates the basis behind one such predictive model linking hypermethylation of the UBB ubiquitin gene to a dependency on UBC and provides a foundation for a cancer dependency map that facilitates the prioritization of therapeutic targets.
Journal ArticleDOI
Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR.
Maximilian Haeussler,Kai Schönig,Helene Eckert,Alexis Eschstruth,Joffrey Mianné,Jean-Baptiste Renaud,Sylvie Schneider-Maunoury,Alena Shkumatava,Lydia Teboul,Jim Kent,Jean-Stéphane Joly,Jean-Paul Concordet +11 more
TL;DR: It is found that the optimal on-target efficiency prediction model strongly depends on whether the guide RNA is expressed from a U6 promoter or transcribed in vitro, and it is demonstrated that the best predictions can significantly reduce the time spent on guide screening.
Journal ArticleDOI
Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells.
Robin M. Meyers,Jordan Bryan,James M. McFarland,Barbara A. Weir,Ann E. Sizemore,Han Xu,Neekesh V. Dharia,Phillip G. Montgomery,Glenn S. Cowley,Sasha Pantel,Amy Goodale,Yenarae Lee,Levi D. Ali,Guozhi Jiang,Rakela Lubonja,William F. Harrington,Matthew Strickland,Ting Wu,Derek C. Hawes,Victor A. Zhivich,Meghan R. Wyatt,Zohra Kalani,Jaime J. Chang,Michael Okamoto,Kimberly Stegmaier,Todd R. Golub,Jesse S. Boehm,Francisca Vazquez,Francisca Vazquez,David E. Root,William C. Hahn,Aviad Tsherniak +31 more
TL;DR: CERES, a computational method to estimate gene-dependency levels from CRISPR–Cas9 essentiality screens while accounting for the copy number–specific effect, is developed and found that CERES decreased false-positive results and estimated sgRNA activity for both this data set and previously published screens performed with different sg RNA libraries.
Journal ArticleDOI
Architecture of the human interactome defines protein communities and disease networks
Edward L. Huttlin,Raphael J. Bruckner,Joao A. Paulo,Joe R. Cannon,Lily Ting,Kurt Baltier,Greg Colby,Fana Gebreab,Melanie P. Gygi,Hannah Parzen,John Szpyt,Stanley Tam,Gabriela Zarraga,Laura Pontano-Vaites,Sharan Swarup,Anne E. White,Devin K. Schweppe,Ramin Rad,Brian K. Erickson,Robert A. Obar,Robert A. Obar,K. G. Guruharsha,Kejie Li,Spyros Artavanis-Tsakonas,Spyros Artavanis-Tsakonas,Steven P. Gygi,J. Wade Harper +26 more
TL;DR: With more than 56,000 candidate interactions, BioPlex 2.0 exceeds previous experimentally derived interaction networks in depth and breadth, and will be a valuable resource for exploring the biology of incompletely characterized proteins and for elucidating larger-scale patterns of proteome organization.
References
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