Genetic and proteomic interrogation of lower confidence candidate genes reveals signaling networks in β-catenin-active cancers

Joseph Rosenbluh, Johnathan Mercer, Yashaswi Shrestha, Rachel Oliver, Pablo Tamayo, John G. Doench, Itay Tirosh, Federica Piccioni, Ella Hartenian, Heiko Horn, Lola Fagbami, David E. Root, Jacob Jaffe, Kasper Lage, Jesse S. Boehm, William C. Hahn

Research output: Contribution to journalArticleResearchpeer-review

13 Citations (Scopus)

Abstract

Genome-scale expression studies and comprehensive loss-of-function genetic screens have focused almost exclusively on the highest confidence candidate genes. Here, we describe a strategy for characterizing the lower confidence candidates identified by such approaches. We interrogated 177 genes that we classified as essential for the proliferation of cancer cells exhibiting constitutive β-catenin activity and integrated data for each of the candidates, derived from orthogonal short hairpin RNA (shRNA) knockdown and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9-mediated gene editing knockout screens, to yield 69 validated genes. We then characterized the relationships between sets of these genes using complementary assays: medium-throughput stable isotope labeling by amino acids in cell culture (SILAC)-based mass spectrometry, yielding 3,639 protein-protein interactions, and a CRISPR-mediated pairwise double knockout screen, yielding 375 combinations exhibiting greater- or lesser-than-additive phenotypic effects indicating genetic interactions. These studies identify previously unreported regulators of β-catenin, define functional networks required for the survival of β-catenin-active cancers, and provide an experimental strategy that may be applied to define other signaling networks.
Original languageEnglish
Pages (from-to)302-316
Number of pages15
JournalCell Systems
Volume3
Issue number3
DOIs
Publication statusPublished - 28 Sep 2016
Externally publishedYes

Keywords

  • CRISPR-Cas9
  • genetic interactions
  • protein-protein interactions
  • RNAi
  • β-catenin

Cite this

Rosenbluh, Joseph ; Mercer, Johnathan ; Shrestha, Yashaswi ; Oliver, Rachel ; Tamayo, Pablo ; Doench, John G. ; Tirosh, Itay ; Piccioni, Federica ; Hartenian, Ella ; Horn, Heiko ; Fagbami, Lola ; Root, David E. ; Jaffe, Jacob ; Lage, Kasper ; Boehm, Jesse S. ; Hahn, William C. / Genetic and proteomic interrogation of lower confidence candidate genes reveals signaling networks in β-catenin-active cancers. In: Cell Systems. 2016 ; Vol. 3, No. 3. pp. 302-316.
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abstract = "Genome-scale expression studies and comprehensive loss-of-function genetic screens have focused almost exclusively on the highest confidence candidate genes. Here, we describe a strategy for characterizing the lower confidence candidates identified by such approaches. We interrogated 177 genes that we classified as essential for the proliferation of cancer cells exhibiting constitutive β-catenin activity and integrated data for each of the candidates, derived from orthogonal short hairpin RNA (shRNA) knockdown and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9-mediated gene editing knockout screens, to yield 69 validated genes. We then characterized the relationships between sets of these genes using complementary assays: medium-throughput stable isotope labeling by amino acids in cell culture (SILAC)-based mass spectrometry, yielding 3,639 protein-protein interactions, and a CRISPR-mediated pairwise double knockout screen, yielding 375 combinations exhibiting greater- or lesser-than-additive phenotypic effects indicating genetic interactions. These studies identify previously unreported regulators of β-catenin, define functional networks required for the survival of β-catenin-active cancers, and provide an experimental strategy that may be applied to define other signaling networks.",
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author = "Joseph Rosenbluh and Johnathan Mercer and Yashaswi Shrestha and Rachel Oliver and Pablo Tamayo and Doench, {John G.} and Itay Tirosh and Federica Piccioni and Ella Hartenian and Heiko Horn and Lola Fagbami and Root, {David E.} and Jacob Jaffe and Kasper Lage and Boehm, {Jesse S.} and Hahn, {William C.}",
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Rosenbluh, J, Mercer, J, Shrestha, Y, Oliver, R, Tamayo, P, Doench, JG, Tirosh, I, Piccioni, F, Hartenian, E, Horn, H, Fagbami, L, Root, DE, Jaffe, J, Lage, K, Boehm, JS & Hahn, WC 2016, 'Genetic and proteomic interrogation of lower confidence candidate genes reveals signaling networks in β-catenin-active cancers', Cell Systems, vol. 3, no. 3, pp. 302-316. https://doi.org/10.1016/j.cels.2016.09.001

Genetic and proteomic interrogation of lower confidence candidate genes reveals signaling networks in β-catenin-active cancers. / Rosenbluh, Joseph; Mercer, Johnathan; Shrestha, Yashaswi; Oliver, Rachel; Tamayo, Pablo; Doench, John G.; Tirosh, Itay; Piccioni, Federica; Hartenian, Ella; Horn, Heiko; Fagbami, Lola; Root, David E.; Jaffe, Jacob; Lage, Kasper; Boehm, Jesse S.; Hahn, William C.

In: Cell Systems, Vol. 3, No. 3, 28.09.2016, p. 302-316.

Research output: Contribution to journalArticleResearchpeer-review

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AU - Rosenbluh, Joseph

AU - Mercer, Johnathan

AU - Shrestha, Yashaswi

AU - Oliver, Rachel

AU - Tamayo, Pablo

AU - Doench, John G.

AU - Tirosh, Itay

AU - Piccioni, Federica

AU - Hartenian, Ella

AU - Horn, Heiko

AU - Fagbami, Lola

AU - Root, David E.

AU - Jaffe, Jacob

AU - Lage, Kasper

AU - Boehm, Jesse S.

AU - Hahn, William C.

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