Journal: NAR Cancer
Article Title: RNA kinetics influence the response to transcriptional perturbation in leukaemia cell lines
doi: 10.1093/narcan/zcae039
Figure Lengend Snippet: Dual targeting of CDK9 and ELAVL1 is synergistic in the THP-1 AML cell line. ( A ) Scatter plot of change in sgRNA read counts in CDK9i compared to untreated (UT) CRISPR-Cas9 genome-wide screening groups after 21 days of passaging in THP-1 and MV4;11 AML cell lines. Annotated RBPs that are down-regulated (logFC <−1) in both THP-1 and MV;11 cell lines indicated in blue and red (ELAVL1). Data is obtained from ( 72 ). ( B ) Western blot of (top) ELAVL1 and (bottom) Laminin B1 protein with indicated treatments and THP-1 cell lines after four days. Image is representative of three biological replicates. ( C ) Simplified schematic of competition assay experimental design. THP-1 cells expressing Cas9 and non-targeting control sgRNA (SCR) and sgRNAs targeting ELAVL1 (ELAVL1 knockout) are mixed in a 1:1 ratio and passaged in the presence of DMSO or CDK9i. ( D ) Fold change relative to day 0 of THP1 ELAVL1 knockout cells in competition with SCR cells as described in (C) at time points and treatments indicated. Values are mean with error bars representing standard deviation (sd) of three biological replicates. Data was analysed using a two-way ANOVA. Ns: P -value not significant. ( E ) (Left) Boxplot of spike-in normalized total mRNA reads with CDK9i relative to DMSO in THP-1 SCR and ELAVL1 KO cells. (Right) Scatter plot of significance and difference in spike-in normalized total gene expression of CDK9i response in ELAVL1 knockout relative to SCR cells. Significantly down- and up-regulated genes are highlighted in blue and red, respectively. ( F ) (Left) Stacked bar chart of previously determined transcript half-life pentiles in THP-1 cells across mRNAs sensitized to CDK9i upon ELAVL1 knockout (lower in KO; logFC < −1 and adjusted P Value < 0.01) and (Right) associated boxplot and ( G ) dot plot of THP-1 gene dependency scores from the Broad Institute Cancer Dependancy Map. LogFC values in each cell line are indicated. ( H ) Bar plot of THP-1 cell death (propidium iodide (PI) positive) in response to CDK9i and MS-444 at concentrations indicated following 72 h. Values are mean with error bars representing standard deviation (sd) of two biological replicates in technical triplicate. Data was analysed using a two-way ANOVA. **** and **: P -Value < 0.0001 and 0.01, respectively. ( I ) ZIP synergy scores derived from (H). Representative of first replicate. ( J ) Gene set enrichment analysis (GSEA) of genes significantly down-regulated with CDK9i in ELAVL1 knockout cells ranked using MS444 and CDK9i versus CDK9i RNA-seq data. NES: normalized enrichment score.
Article Snippet: Independent sgRNAs targeting ELAVL1 and non-targeting sgRNA controls (SCR; ) flanked with BsmBI overhangs were ligated into the vector FgH1tUTG-GFP (Addgene Plasmid #70183) using 1uL BsmBI (New England Biolabs, R0739) in NEBuffer 3.1 (New England Biolabs, B7203S).
Techniques: CRISPR, Genome Wide, Passaging, Western Blot, Competitive Binding Assay, Expressing, Control, Knock-Out, Standard Deviation, Gene Expression, Derivative Assay, RNA Sequencing
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