Journal: Nature Communications

Article Title: A pan-CRISPR analysis of mammalian cell specificity identifies ultra-compact sgRNA subsets for genome-scale experiments

doi: 10.1038/s41467-022-28045-w

Figure Lengend Snippet: a Schematic illustrating difference between classic synthetic lethality and our common genetic architecture . Synthetic lethality consists of many individual Y i functions. These functions are cell-type-specific models with single features. Our proposed common genetic architecture is hypothesized to connect these “private” functions with shared CERES features. A common genetic architecture has many redundant edges, and more interconnected nodes. More nodes suggest that more cell-type-specific phenotypes are predictable, and more edges suggest redundancy. b A network built from the aggregation of all multivariate models. Genes are represented as nodes and feature-target gene relations as edges. Colors represent distinct subnetwork communities that were identified by the Louvain method. c Network communities with (right) and without (left) nodes/edges involving functional CRISPR features for a single Louvain community, and a comparison with our hypothesis from ( a ). Edges are colored based upon the data source; and nodes are colored based on the model score (of top ten feature model) of the corresponding gene as target. d To quantitate the visual similarity between our hypothesis in ( a ) and the data in ( c ) across all Louvain communities, we examined the differences in the clustering coefficient, the average number of neighbors, and the network heterogeneity. e gprofiler2 plots examine the enrichment of functional categories. f Residual plot identifies GO terms that are more (residuals of −log10 P values >10) or less (residuals of -log10 P values < −10) enriched in predictor genes than in target genes. Dots represent shared GO terms among the 100 most significant terms in target and predictor gprofiler2 analysis result. The p- values from gprofiler2 for ( e ) and ( f ) are based on hypergeometric tests with multiple testing corrections using the g:SCS method. Source data are provided as a Source Data file.

Article Snippet: Human Brunello CRISPR knockout pooled library was a gift from David Root and John Doench (Addgene #73178).

Techniques: Functional Assay, CRISPR, Comparison

Journal: Nature Communications

Article Title: A pan-CRISPR analysis of mammalian cell specificity identifies ultra-compact sgRNA subsets for genome-scale experiments

doi: 10.1038/s41467-022-28045-w

Figure Lengend Snippet: a Two separate pooled screens were performed in a cell line (PC9) that was not included in model training and validation. Experiment 1 was the full Brunello library. A 21-day dropout experiment was performed in PC9 cells. Measurements on 18,114 genes were direct and form the gold standard. The L200 can be computationally extracted from the full screen and compared to these gold-standard measurements. A new L200 standalone library of 800 guides targeting 200 genes was cloned. This library can be used to perform a small-scale lossy compression experiment. The data can then be compared to the gold standard. b Correlations of inferred vs measured CERES scores for both screens in ( a ) and a comparison of the predictions between the standalone sets and the computationally extracted L200 set in the Brunello library. c A Venn diagram describes the overlap in “Hits” in the 500 most differentially required genes for growth in PC9 cells. Both of the lossy compression screens from ( a ) and the gold-standard (measured) data are compared. Source data are provided as a Source Data file.

Article Snippet: Human Brunello CRISPR knockout pooled library was a gift from David Root and John Doench (Addgene #73178).

Techniques: Biomarker Discovery, Clone Assay, Comparison

Journal: Hepatology (Baltimore, Md.)

Article Title: Depletion of TRRAP Induces p53-Independent Senescence in Liver Cancer by Down-Regulating Mitotic Genes.

doi: 10.1002/hep.30807

Figure Lengend Snippet: Figure 1. A kinome CRISPR screen identifies TRRAP as an essential gene for HCC cell growth. A) Three HCC cell lines were used to identify genes whose depletion inhibit HCC proliferation. Eight candidate genes were identified by integrating CRISPR screen results with HCC patient data. B) Genes from the CRISPR screen were ranked by their false discovery rate, the 8 candidate genes are indicated. C) mRNA levels of TRRAP in non- tumor and tumor samples from the GSE14520 (left) and TCGA (right) data sets, p-values were calculated using moderated t-test and Wilcoxon signed-rank test respectively. Black lines indicate the geometric mean of each group. D) Kaplan Meier curves of HCC patients from the TCGA (left) and NIH Laboratory of Experiment Carcinogenesis (LEC, right) cohorts with high (TCGA n=115 and LEC n=31) or low (TCGA n=118 and LEC n=31) TRRAP expression. P-values were calculated using the log-rank Mantel-Cox test. *p < 0.05, ***p < 0.001.

Article Snippet: Kinome CRISPR screen The human kinome CRISPR pooled library was a gift from John Doench and David Root (Addgene #1000000083).

Techniques: CRISPR, Expressing

Journal: Hepatology (Baltimore, Md.)

Article Title: Depletion of TRRAP Induces p53-Independent Senescence in Liver Cancer by Down-Regulating Mitotic Genes.

doi: 10.1002/hep.30807

Figure Lengend Snippet: Figure 4. Senescence induced by TRRAP and KAT5 depletion is independent of p21. A) Schematic illustrating generation of p21 and TRRAP/KAT5 double knockout cells using CRISPR. B) Western blot analysis of TRRAP, KAT5 and p21 levels in Huh7 and SNU-475 cells infected with the indicated sgRNAs. C) Colony formation and SA-β-gal staining of Huh7 cells infected with the indicated sgRNAs. NS = not significant (student’s t test).

Article Snippet: Kinome CRISPR screen The human kinome CRISPR pooled library was a gift from John Doench and David Root (Addgene #1000000083).

Techniques: Double Knockout, CRISPR, Western Blot, Infection, Staining

Journal: PLoS ONE

Article Title: Considerations and practical implications of performing a phenotypic CRISPR/Cas survival screen

doi: 10.1371/journal.pone.0263262

Figure Lengend Snippet: (A) Viability staining of DIE cells treated with doxycycline (Doxy) concentrations (100, 250, 500 or 1000ng/ml) and for different exposure times (2, 4, 6, or 8h) to determine the optimal concentration and exposure time to induce sufficient cell death rates in DIE cells. Green circles indicate which conditions (low Doxy: 250ng/ml high Doxy: 1000ng/ml); were used for the genome-wide CRIPSR/Cas9 screen. (B) The CRISPR/Cas9 screen timeline from the time of library transfection (Day 0) to the final harvest of surviving DIE cells (Day 10). 6 days after transfection of the library, Doxycycline (Doxy) was added for 24h to induce DUX4 expression. Low Doxy: 250ng/ml; high Doxy: 1000ng/ml; early harvest: 24h after Doxy removal; late harvest: 48h after Doxy removal. (C) Volcano plot showing the enrichment of sets of guides of the low doxycycline 250ng/ml) -early harvest (24h after doxycycline removal) screen (early-low). Blue points represent guide sets that are significantly enriched (P-value ≤ 0.01), LFC ≥ 1), green points are the positive controls (DUX4, MAST1, MGAT4B), red points represent the non-target/negative control guides. (D) Chromosomal ideogram indicating the location of enriched hits in the human genome, of the low doxycycline-early harvest screen (see panel B). (E) Schematic representation of the location of a small number of false positive hits on chromosome 5 and chromosome 19. (F) Viability staining demonstrating surviving DIE-Cas9 cells (DIE cells constitutively expressing Cas9) after 250ng/ml doxycycline exposure, containing knockouts of the same genes mentioned in (E), but also DUX4, MGAT4B and MAST1. Media did not contain any selection markers (blasticidin or puromycin) to select for the presence of the rtTA3 or the DUX4 transgene. NT: Non-target controls.

Article Snippet: The Human Brunello CRISPR knockout pooled lentiviral prep library was a gift from David Root and John Doench (Broad Institute, MA, U.S.A.).

Techniques: Staining, Concentration Assay, Genome Wide, CRISPR, Transfection, Expressing, Negative Control, Selection

Journal: PLoS ONE

Article Title: Considerations and practical implications of performing a phenotypic CRISPR/Cas survival screen

doi: 10.1371/journal.pone.0263262

Figure Lengend Snippet: (A) Adjusted volcano plot of screen data with low doxycycline (250ng/ml)/early harvest (24h after doxycycline removal, see ) showing the enrichment of sets of guides targeting genes not located on chromosome 5q or chromosome 19p. Blue points represent guide sets that are significantly enriched (P-value ≤ 0.01), Log2(fold change) ≥ 1), the green point is the positive control (DUX4), red points represent the non-target control guides. (B) Venn diagram showing the overlap of filtered hits between the four screens (EL: Early harvest-low Doxy, LL: Late harvest-Low doxy, EH: Early harvest-high Doxy, LH: Late harvest-High doxy), see also . (C) Viability staining showing surviving DIE cells containing single knockouts of potentials hits, identified in the CRISPR screen. Knockouts of individual genes were generated by transfection of sgRNA; 6 days later, cells were left untreated or treated with 3 different concentrations of doxycycline (100, 250 and 1000ng/ml) for and incubated for an additional 48–96 hours prior to visualizing surviving cells. Data are representative of at least three independent experiments. (D) Viability staining showing the surviving DIE-ieGFP-Cas9 cells (DIE cells expressing Cas9 constitutively and contain doxycycline-inducible eGFP) with single knockouts of mediator complex subunits. Knockouts of individual genes were generated by transfection of sgRNA; 6 days later cells were treated for doxycycline (250ng/ml) for 24h and incubated for an additional 48–96 hours prior to visualizing surviving cells. Data are representative of at least three independent experiments. (E) FACS data showing GFP-positive cells in surviving populations of DIE-ieGFP-Cas9 (expressing constitutive Cas9 and doxycycline-inducible GFP). cells containing single knockouts as indicated. Knockouts of individual genes were generated by transfection of sgRNA; 6 days later, cells were treated with doxycycline (250ng/ml) for 24h prior to FACS analysis. DIE-ieGFP-Cas9 cells comprised of 42% of eGFP-positive cells after DUX4 knockout. rtTA, MED25, MED24 and MED16 knockouts displayed a lower percentage of eGFP-expressing cells, comprising between 1.2–4% of eGFP-expressing cells. Data are representative of at least three independent experiments.

Article Snippet: The Human Brunello CRISPR knockout pooled lentiviral prep library was a gift from David Root and John Doench (Broad Institute, MA, U.S.A.).

Techniques: Positive Control, Control, Staining, CRISPR, Generated, Transfection, Incubation, Expressing, Knock-Out