![Figure 4. Gene expression profiling after THZ1 treatment in ATL cells. (A-B) Metagene representation of global Pol II occupancy in TL-Om1 cells spanning 2 kb upstream of the TSS to 2 kb downstream of the TES for super-enhancer (SE)–associated genes (A) or typical enhancer (TE)–associated genes (B) in control (blue) and THZ1-treated samples (red). The inset is a magnification of the region from the TES to 2 kb downstream. (C) The ChIP-seq gene tracks represent Pol II signals in the TL-Om1 cell line after control or THZ1 treatment at the CCR4 and TNFRSF8/CD30 gene loci. (D) MA-plot of differentially expressed genes (annotated genes only) in the control and THZ1-treated TL-Om1 cells based on microarray analysis. The y-axis indicates the log2 fold change in gene expression. The x-axis indicates the log2 mean normalized expression (robust multiarray algorithm) of 3 DMSO-treated control samples. The green dots represent differentially expressed genes with a value of P < .05. The blue dots represent significantly downregulated genes (false discovery rate <0.001, log2 fold change <−1). Among the significantly downregulated genes, the genes associated with super-enhancers in TL-Om1 cells are shown by red dots. (E) GSEA to determine the correlation of super-enhancers with gene expression changes on treatment with THZ1 in TL-Om1 cells. The GSEA plot indicates the degree to which SE-associated genes are overrepresented at the extreme left (downregulated by THZ1) or right (upregulated by THZ1) of the entire ranked list. Solid bars represent super-enhancer–associated genes. (F) The mRNA expression levels of CCR4, TNFRSF8/CD30, PLCG1, and PRKCB in TL-Om1 cells treated with or without THZ1 were analyzed by microarray analysis, and the results are shown as a percentage of the DMSO-treated control. The data are presented as the mean ± standard deviation of triplicate experiments. (G) CCR4 and TNFRSF8/CD30 mRNA expression levels in 2 THZ1-sensitive (TL-Om1 and ATL-55T[–]) and 2 THZ1-resistant (MT-2 and ATL-43b[−]) cell lines were analyzed by qRT-PCR. The results are shown as a percentage of the DMSO-treated control. The data are presented as the mean ± standard deviation of duplicate experiments. *P < .05, **P < .01, ***P < .001 by 2-sample, 2-tailed Student t test compared with the DMSO-treated control.](https://ash.silverchair-cdn.com/ash/content_public/journal/blood/130/21/10.1182_blood-2017-06-792184/4/blood792184f4.jpeg?Expires=1726825309&Signature=PJQtvOY8WPniyZutB-0YImwICpu8Syp0z5sGml-MSFo8HPY9ELLaTjz7k~d-qOAEMkZCFvT8oZfaW4uq2U4xXG9R1BV3LBY2JxEo~QXckK6CajS0ioEJ2G4jv~8kImYcWdhFrIFl7ahdMy7wPrl0HwzD0432DXw-RkVzOiLhsDA5lWvsytygdxIQGz2E6qJabGfAFfas1TFLrf7CTNTbXgGgdlsvNqg78rIDoKj5pwGNoI33CIEIQwH6BI~TA7BLlGj~fwDbIFLCOaXm9vc00T~rRLDheapaxyWL4rw9~cDOKr9M~aycwaRBSFxRWye-V2OeMK9MO2PBNHOas0YjWg__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA)
Gene expression profiling after THZ1 treatment in ATL cells. (A-B) Metagene representation of global Pol II occupancy in TL-Om1 cells spanning 2 kb upstream of the TSS to 2 kb downstream of the TES for super-enhancer (SE)–associated genes (A) or typical enhancer (TE)–associated genes (B) in control (blue) and THZ1-treated samples (red). The inset is a magnification of the region from the TES to 2 kb downstream. (C) The ChIP-seq gene tracks represent Pol II signals in the TL-Om1 cell line after control or THZ1 treatment at the CCR4 and TNFRSF8/CD30 gene loci. (D) MA-plot of differentially expressed genes (annotated genes only) in the control and THZ1-treated TL-Om1 cells based on microarray analysis. The y-axis indicates the log2 fold change in gene expression. The x-axis indicates the log2 mean normalized expression (robust multiarray algorithm) of 3 DMSO-treated control samples. The green dots represent differentially expressed genes with a value of P < .05. The blue dots represent significantly downregulated genes (false discovery rate <0.001, log2 fold change <−1). Among the significantly downregulated genes, the genes associated with super-enhancers in TL-Om1 cells are shown by red dots. (E) GSEA to determine the correlation of super-enhancers with gene expression changes on treatment with THZ1 in TL-Om1 cells. The GSEA plot indicates the degree to which SE-associated genes are overrepresented at the extreme left (downregulated by THZ1) or right (upregulated by THZ1) of the entire ranked list. Solid bars represent super-enhancer–associated genes. (F) The mRNA expression levels of CCR4, TNFRSF8/CD30, PLCG1, and PRKCB in TL-Om1 cells treated with or without THZ1 were analyzed by microarray analysis, and the results are shown as a percentage of the DMSO-treated control. The data are presented as the mean ± standard deviation of triplicate experiments. (G) CCR4 and TNFRSF8/CD30 mRNA expression levels in 2 THZ1-sensitive (TL-Om1 and ATL-55T[–]) and 2 THZ1-resistant (MT-2 and ATL-43b[−]) cell lines were analyzed by qRT-PCR. The results are shown as a percentage of the DMSO-treated control. The data are presented as the mean ± standard deviation of duplicate experiments. *P < .05, **P < .01, ***P < .001 by 2-sample, 2-tailed Student t test compared with the DMSO-treated control.
