Journal: Molecular Cancer

Article Title: The lncRNA CASC15 regulates SOX4 expression in RUNX1-rearranged acute leukemia

doi: 10.1186/s12943-017-0692-x

Figure Lengend Snippet: CASC15 knockdown leads to enrichment for the transcriptional program of SOX4 and YY1 . a Unsupervised hierarchical gene clustering of differentially expressed genes upon CASC15 siRNA mediated knockdown in RS4;11 cells (PPDE >99%, fold change >2). b - g RT-qPCR confirmation of differentially expressed genes from the microarray in RS4;11 ( b - d ) and REH ( e - g ) cell lines. h To narrow down transcription factors that might be responsible for the observed changes in gene expression, we overlapped transcription factors that were associated with the differentially expressed gene sets in CASC15 KD RS4;11 cells as well as CASC15 KO REH cells. Shown are the numbers of genes in the differentially expressed gene set for each transcription factor that showed an association. i - j Enrichment plots from gene set enrichment analysis (GSEA). The differentially regulated gene set from CASC15 KD RS4;11 cells showed a positive enrichment score when compared to genes up-regulated in ACC3 cells with SOX4 knockdown ( i ; Enrichment Score = 0.5, FDRq = 0.0 and P value = 0.0), and showed a negative enrichment score when compared to genes downregulated in ACC3 cells with SOX4 knockdown ( j ; Enrichment Score = −0.38,FDRq = .017 and P value = 0.01). k - l Enrichment plots from gene set enrichment analysis (GSEA) showing that the differentially regulated gene set showed a positive enrichment score when compared with upregulated genes upon YY1 knockdown ( k ; Enrichment Score = 0.5, FDRq = 0 and P value = 0.0) and a negative enrichment score with downregulated genes upon YY1 knockdown ( l ; Enrichment Score = -0.39, FDRq = 0 and P value = 0.0)

Article Snippet: Pre-cleared lysate was divided into two and incubated overnight with gentle rotation at 4 °C with the YY1 antibody (Rabbit mAb #2185: Cell signaling) and the normal IgG.

Techniques: Knockdown, Quantitative RT-PCR, Microarray, Gene Expression

Journal: Molecular Cancer

Article Title: The lncRNA CASC15 regulates SOX4 expression in RUNX1-rearranged acute leukemia

doi: 10.1186/s12943-017-0692-x

Figure Lengend Snippet: CASC15 regulates the activity of YY1 on the SOX4 promoter. a Transcriptional activity of SOX4 promoter upon CASC15 (L) and/or YY1 overexpression, as measured by dual luciferase assay. Luciferase values are normalized to the empty vector. b - d RT-qPCR with primers directed against SOX 4 (b) CASC15 ( c ) and YY1 ( d ) and Western blot for YY1 ( e ) in 293 T cells transiently transfected with YY1 and CASC15 . All qPCR analyses for CASC15 were performed with primer set #1 and normalized to GAPDH or actin, except where otherwise noted. Experiments were repeated three times for validation

Article Snippet: Pre-cleared lysate was divided into two and incubated overnight with gentle rotation at 4 °C with the YY1 antibody (Rabbit mAb #2185: Cell signaling) and the normal IgG.

Techniques: Activity Assay, Over Expression, Luciferase, Plasmid Preparation, Quantitative RT-PCR, Western Blot, Transfection, Biomarker Discovery