GSE97435
USP7 controls the oncogenic transcriptional circuitry and is a novel therapeutic target in T cell leukemia
T-cell acute lymphoblastic leukemia (T-ALL) is an immature hematopoietic malignancy driven mainly by oncogenic activation of NOTCH1 signaling. In this study we chemically inhibited the deubiquinating enzyme USP7 and assayed for gene expression changes. This piece of data was further integrated to epigenetic changes using ChIP-Sequencing analysis of H3K27me3, H2AUb, H2BUb, H3K27Ac and H3K79me2 upon inhibition of USP7. These results coupled helped to determine the role of USP7 in stabilizing and promoting T-ALL leukemia. We also compared the gene expression and epigenetic changes of USP7 inhibition with inhibition of NOTCH1 pathway and JMJD3. Overall design: [USP7 ChIP]: 10 million cells were used for the ChIP and precipitated using antibody against USP7 (Bethyl, A300-033A). [H3K79me2 ChIP]: 10 million cells were used for the ChIP and precipitated using antibody against H3K79me2 (homemade, Ali Shilatifard lab) [H3K27me3 ChIP]: 10 million cells were used for the ChIP and precipitated using antibody against H3K27me3 (Cell Signaling Technology, 9733S). [H2AUb ChIP]: 10 million cells were used for the ChIP and precipitated using antibody against H2AUb (Cell Signaling Technology, 8240S). [H2BUb ChIP]: 10 million cells were used for the ChIP and precipitated using antibody against H2BUb (Cell Signaling Technology, 5546S). [H3K27Ac ChIP]: 10 million cells were used for the ChIP and precipitated using antibody against H3K27Ac (Cell Signaling Technology, 8173S). [RNA-Seq]: 1-5 million primary cells from CUTLL1 human T cell leukemia cells treated with the following inhibitor: 1 micromolar USP7 inhibitor, 1 micromolar GSI, 2 micromolar GSKJ4 and 1 micromolar DMSO. [RNA-Seq]: 1-5 million primary cells from JURKAT human T cell leukemia cells treated with the following inhibitor: 1 micromolar USP7 inhibitor and 1 micromolar DMSO. [RNA-Seq]: 3-5 million primary cells from JURKAT human T cell leukemia cells treated with shUSP7 or empty vector (PLKO). [RNA-Seq]: 1-5 million primary cells from JURKAT human T cell leukemia cells treated with the following inhibitors: 1 micromolar GSI, 500 nanomolar JQ1, and 1 micromolar DMSO.