A probability-based approach for the analysis of large-scale RNAi screens

König, Renate; Chiang, Chih-Yuan; Tu, Buu P.; Yan, S. Frank; DeJesus, Paul; Romero, Angélica; Bergauer, Tobias; Orth, Anthony P.; Krueger, Ute; Zhou, Yingyao; Chanda, Sumit K.

doi:10.1038/nmeth1089

Cited by 329 publications

(370 citation statements)

References 15 publications

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“…S1B and Methods and Dataset S2 for a detailed description of these calculations). In addition to scoring the individual shRNAs, we derived gene level calls from the 17 shRNAs for each gene by applying the Redundant siRNA Activity (RSA) algorithm, which calculates gene-centric P values (23). To identify genes whose product is selectively required for growth in a subset of cancer lines, we performed k-means clustering (24) of the RSA value for each gene to define groups of "sensitive" and "insensitive" cell lines and subsequently ranked hits based on the difference in cluster centers (SI Appendix, Methods).…”

Section: Resultsmentioning

confidence: 99%

Functional epigenetics approach identifies BRM/SMARCA2 as a critical synthetic lethal target in BRG1-deficient cancers

Hoffman¹,

Rahal²,

Buxton³

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

352

315

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Defects in epigenetic regulation play a fundamental role in the development of cancer, and epigenetic regulators have recently emerged as promising therapeutic candidates. We therefore set out to systematically interrogate epigenetic cancer dependencies by screening an epigenome-focused deep-coverage design shRNA (DECODER) library across 58 cancer cell lines. This screen identified BRM/SMARCA2, a DNA-dependent ATPase of the mammalian SWI/ SNF (mSWI/SNF) chromatin remodeling complex, as being essential for the growth of tumor cells that harbor loss of function mutations in BRG1/SMARCA4. Depletion of BRM in BRG1-deficient cancer cells leads to a cell cycle arrest, induction of senescence, and increased levels of global H3K9me3. We further demonstrate the selective dependency of BRG1-mutant tumors on BRM in vivo. Genetic alterations of the mSWI/SNF chromatin remodeling complexes are the most frequent among chromatin regulators in cancers, with BRG1/SMARCA4 mutations occurring in ∼10-15% of lung adenocarcinomas. Our findings position BRM as an attractive therapeutic target for BRG1 mutated cancers. Because BRG1 and BRM function as mutually exclusive catalytic subunits of the mSWI/SNF complex, we propose that such synthetic lethality may be explained by paralog insufficiency, in which loss of one family member unveils critical dependence on paralogous subunits. This concept of "cancerselective paralog dependency" may provide a more general strategy for targeting other tumor suppressor lesions/complexes with paralogous subunits.

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Section: Resultsmentioning

confidence: 99%

Functional epigenetics approach identifies BRM/SMARCA2 as a critical synthetic lethal target in BRG1-deficient cancers

Hoffman¹,

Rahal²,

Buxton³

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

352

315

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“…This screen, previously developed in our laboratory, already led to the discovery of a new role for BRCA2 and PALB2 in checkpoint signalling 14 . Data from the screen were statistically analysed to identify candidate genes 15 ( Supplementary Fig. 1a-c).…”

Section: Resultsmentioning

confidence: 99%

“…The data obtained from the screen was submitted to a redundant siRNA activity analysis that models the probability of a gene 'hit' based on the collective activities of multiple siRNAs per gene 15 . Using this method, the siRNAs were ranked according to their score.…”

Section: Methodsmentioning

confidence: 99%

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Cyclin F suppresses B-Myb activity to promote cell cycle checkpoint control

et al. 2015

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Cells respond to DNA damage by activating cell cycle checkpoints to delay proliferation and facilitate DNA repair. Here, to uncover new checkpoint regulators, we perform RNA interference screening targeting genes involved in ubiquitylation processes. We show that the F-box protein cyclin F plays an important role in checkpoint control following ionizing radiation. Cyclin F-depleted cells initiate checkpoint signalling after ionizing radiation, but fail to maintain G2 phase arrest and progress into mitosis prematurely. Importantly, cyclin F suppresses the B-Myb-driven transcriptional programme that promotes accumulation of crucial mitosis-promoting proteins. Cyclin F interacts with B-Myb via the cyclin box domain. This interaction is important to suppress cyclin A-mediated phosphorylation of B-Myb, a key step in B-Myb activation. In summary, we uncover a regulatory mechanism linking the F-box protein cyclin F with suppression of the B-Myb/cyclin A pathway to ensure a DNA damage-induced checkpoint response in G2.

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“…Hits were identified as those with a median IC 50 shift of median IC 50 AE 3MAD (median absolute deviations) or greater (11,12). To assign statistical significance to siRNA hits identified from the siRNA screen, we then modeled the collective activities of the 4 individual siRNAs used for each gene by using redundant siRNA activity (RSA) analysis (13). Briefly, the normalized, log 2 transformed IC 50 shifts of all siRNAs were rank ordered and the rank distribution of all siRNAs targeting the same gene was examined and a P value was calculated on the basis of an iterative hypergeometric distribution formula (13).…”

Section: Hit Identification and Statistical Analysismentioning

confidence: 99%

Functional Genomics Reveals Diverse Cellular Processes That Modulate Tumor Cell Response to Oxaliplatin

Harradine

Kassner

Chow

et al. 2011

Molecular Cancer Research

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Oxaliplatin is widely used to treat colorectal cancer, as both adjuvant therapy for resected disease and palliative treatment of metastatic disease. However, a significant number of patients experience serious side effects, including prolonged neurotoxicity, from oxaliplatin treatment creating an urgent need for biomarkers of oxaliplatin response or resistance to direct therapy to those most likely to benefit. As a first step to improve selection of patients for oxaliplatin-based chemotherapy, we have conducted an in vitro cell-based small interfering RNA (siRNA) screen of 500 genes aimed at identifying genes whose loss of expression alters tumor cell response to oxaliplatin. The siRNA screen identified twenty-seven genes, which when silenced, significantly altered colon tumor cell line sensitivity to oxaliplatin. Silencing of a group of putative resistance genes increased the extent of oxaliplatin-mediated DNA damage and inhibited cell-cycle progression in oxaliplatin-treated cells. The activity of several signaling nodes, including AKT1 and MEK1, was also altered. We used cDNA transfection to overexpress two genes (LTBR and TMEM30A) that were identified in the siRNA screen as mediators of oxaliplatin sensitivity. In both instances, overexpression conferred resistance to oxaliplatin. In summary, this study identified numerous putative predictive biomarkers of response to oxaliplatin that should be studied further in patient specimens for potential clinical application. Diverse gene networks seem to influence tumor survival in response to DNA damage by oxaliplatin. Finally, those genes whose loss of expression (or function) is related to oxaliplatin sensitivity may be promising therapeutic targets to increase patient response to oxaliplatin. Mol Cancer Res; 9(2); 173-82. Ó2010 AACR.

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A probability-based approach for the analysis of large-scale RNAi screens

Cited by 329 publications

References 15 publications

Functional epigenetics approach identifies BRM/SMARCA2 as a critical synthetic lethal target in BRG1-deficient cancers

Functional epigenetics approach identifies BRM/SMARCA2 as a critical synthetic lethal target in BRG1-deficient cancers

Cyclin F suppresses B-Myb activity to promote cell cycle checkpoint control

Functional Genomics Reveals Diverse Cellular Processes That Modulate Tumor Cell Response to Oxaliplatin

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