Journal: Oncotarget

Article Title: BH3-mimetics and BET-inhibitors elicit enhanced lethality in malignant glioma

doi: 10.18632/oncotarget.16365

Figure Lengend Snippet: A .- C . U87MG, LN229, T98G established glioblastoma cell lines, GBM39, GBM6 and GBM14 patient-derived xenograft cultures and NCH644 and NCH421k stem cell-like glioma cultures were treated as indicated with JQ1. After 72h of treatment, CellTiter-Glo assays were performed. IC 50 values were calculated. Column: mean. Error bar: standard deviation (SD). n = 3. D ., E ., U87MG, LN229, T98G established glioblastoma cell lines, GBM39, GBM6 and GBM14 patient-derived xenograft cultures were treated with ABT263, JQ1 or the combination of both. After 72h of treatment, CellTiter-Glo assays were performed. Column: mean. Error bar: standard deviation (SD). n = 3. Statistical analysis was performed and p values were calculated. A p-value of less than 0.05 was considered statistically significant. F .- H ., LN229, T98G and NCH644 glioblastoma cells were treated for 72 hours with ABT263, JQ1 or the combination and analyzed by CellTiter-Glo assay. CI values and fraction affected were calculated using the CompuSyn software (ComboSyn, Inc., Paramus, NJ, U.S.A.). Data points located below 1 (CI value less than 1) indicate a synergistic drug-drug interaction and data points larger than 1 indicate an antagonistic drug-drug interaction. Some data points overlap and are therefore not represented on the graphical chart. A colored line highlights CI value 1. For individual values, please refer to Table .

Article Snippet: Notably, stem cell-like glioma cells display a remarkable sensitivity to the drug combination of BET-inhibitors, such as JQ1 and OTX015, and BH3-mimetics.

Techniques: Derivative Assay, Standard Deviation, Glo Assay, Software

Journal: Oncotarget

Article Title: BH3-mimetics and BET-inhibitors elicit enhanced lethality in malignant glioma

doi: 10.18632/oncotarget.16365

Figure Lengend Snippet: CI values for glioblastoma cultures after combinatorial treatments with ABT263 and JQ1

Article Snippet: Notably, stem cell-like glioma cells display a remarkable sensitivity to the drug combination of BET-inhibitors, such as JQ1 and OTX015, and BH3-mimetics.

Techniques:

Journal: Oncotarget

Article Title: BH3-mimetics and BET-inhibitors elicit enhanced lethality in malignant glioma

doi: 10.18632/oncotarget.16365

Figure Lengend Snippet: A ., B ., C . representative histograms of LN229, U87 and T98G glioblastoma cells that were treated for the indicated time points as indicated with JQ1, ABT263 or both prior to staining with propidium iodide and flow cytometric analysis. D .- F ., LN229, U87 and T98G glioblastoma cells were treated for the indicated time points as indicated with OTX015, Obatoclax or the combination. G ., representative histograms of T98G glioblastoma cells treated with ABT263, JQ1 or the combination as indicated for 48h prior to staining for annexin V and propidium iodide and flow cytometric analysis. H ., representative histograms of T98G glioblastoma cells that were treated with JQ1, ABT263, or both prior to staining with TMRE and flow cytometric analysis. I ., T98G glioblastoma cells were treated for 24 h with JQ1, ABT263 or the combination. Whole-cell extracts were examined by Western blot analysis for PARP, cleaved caspase 9 (C9) and cleaved caspase 3. Vinculin Western blot analysis was performed to confirm equal protein loading.

Article Snippet: Notably, stem cell-like glioma cells display a remarkable sensitivity to the drug combination of BET-inhibitors, such as JQ1 and OTX015, and BH3-mimetics.

Techniques: Staining, Western Blot

Journal: Oncotarget

Article Title: BH3-mimetics and BET-inhibitors elicit enhanced lethality in malignant glioma

doi: 10.18632/oncotarget.16365

Figure Lengend Snippet: A ., Established glioblastoma cells, U87,LN229, T98G and stem cell-like glioma cells, NCH644 were treated with increasing concentrations of JQ1 as indicated for 72h. Whole cell extracts were collected and Western blot analysis was performed for Usp9X, Mcl-1, Bcl-2, Bcl-xL, Noxa and Bim. Actin served as loading control. B ., C . U87, LN229 and T98G cells were treated with ABT263, JQ1 or the combination of both for 24h (B) and 48h (C). Whole cell extracts were collected and Western blot analysis was performed for Mcl-1, Bcl-2, Bcl-xL, Noxa and Bim. Actin served as loading control. D ., U87 and LN229 cells were treated with ABT263, JQ1 or the combination of both. After 7h cells were harvested and RNA was isolated. Real-time PCR for Noxa was conducted and the results were normalized to 18S. Column: mean. Error bar: standard error of measurement (SEM). G, LN229 cells were transfected with non-targeting (n.t.) siRNA or an ATF4 specific siRNA. 72h after transfection cells were treated with ABT263 and JQ1 for 7h. Cells were harvested and analyzed by western blotting for ATF4 and Noxa. Actin serves as loading control.

Article Snippet: Notably, stem cell-like glioma cells display a remarkable sensitivity to the drug combination of BET-inhibitors, such as JQ1 and OTX015, and BH3-mimetics.

Techniques: Western Blot, Control, Isolation, Real-time Polymerase Chain Reaction, Transfection

Journal: Oncotarget

Article Title: BH3-mimetics and BET-inhibitors elicit enhanced lethality in malignant glioma

doi: 10.18632/oncotarget.16365

Figure Lengend Snippet: A .- D ., Representative flow plots of LN229 cells that were treated with n.t.-siRNA or 2 different Bcl-xL siRNAs prior to additional treatment with either solvent or JQ1. Staining for propidium iodide and flowcytometric analysis was performed to determine the fraction of subG1 cells. The results were quantified (D). Knockdown of Bcl-xL was confirmed by Western Blot analysis (C). Actin served as loading control (C). E .- G . LN229 cells were treated with n.t.-siRNA or Noxa-siRNA or Bak-siRNA prior to treatment with solvent or the combination of 1μM ABT263 and 5μM JQ1 as indicated for 24 h. Staining for propidium iodide and flow cytometric analysis was performed to determine the fraction of subG1 cells. Representative flow plots are shown (E). The quantifications are shown in (G). Noxa and Bak knockdowns were confirmed by Western blot analysis (F). H ., LN229 cells were transfected with n.t.-siRNA or four individual Mcl-1 siRNAs for 48h. Subsequently, cells were treated with ABT263 and analyzed by CellTiter-Glo assay. The concentrations for ABT263 are in μM. Column: mean. Error bar: standard deviation (SD). I ., LN229 cells were transfected as in G and analyzed for protein expression of Mcl-1. Actin served as a loading control.

Article Snippet: Notably, stem cell-like glioma cells display a remarkable sensitivity to the drug combination of BET-inhibitors, such as JQ1 and OTX015, and BH3-mimetics.

Techniques: Solvent, Staining, Knockdown, Western Blot, Control, Transfection, Glo Assay, Standard Deviation, Expressing

Journal: Oncotarget

Article Title: BH3-mimetics and BET-inhibitors elicit enhanced lethality in malignant glioma

doi: 10.18632/oncotarget.16365

Figure Lengend Snippet: A ., LN229 cells were transfected with n.t.-siRNA or c-myc-siRNA-1 prior to treatment with solvent or ABT263 as indicated for 24 h. Staining for propidium iodide and flow cytometric analysis were performed to determine the fraction of subG1 cells. Representative flow plots are shown. The quantifications are shown in C . c-myc knockdown was confirmed by Western blot analysis B . D ., LN229 cells were transfected with n.t.-siRNA or c-myc-siRNA-2 prior to treatment with solvent or ABT263 as indicated for 24 h. Staining for propidium iodide and flow cytometric analysis were performed to determine the fraction of subG1 cells. Representative flow plots are shown. The quantifications are shown in F . c-myc knockdown was confirmed by Western blot analysis E . G . U87, T98G, LN229 (established glioblastoma cells), NCH644 (stem cell-like glioma cells) and GBM6 (patient-derived xenograft) cells were treated with JQ1 for 72 hours. Protein extracts were prepared and samples were analyzed by conventional western blot analysis for the expression of c-myc. Actin serves as a loading control. Multiple exposures are presented due to the fact that cells express different baseline levels of c-myc. * indicate different exposure times for c-myc protein.

Article Snippet: Notably, stem cell-like glioma cells display a remarkable sensitivity to the drug combination of BET-inhibitors, such as JQ1 and OTX015, and BH3-mimetics.

Techniques: Transfection, Solvent, Staining, Knockdown, Western Blot, Derivative Assay, Expressing, Control

Journal: Nature Communications

Article Title: Enhancer and super-enhancer dynamics in repair after ischemic acute kidney injury

doi: 10.1038/s41467-020-17205-5

Figure Lengend Snippet: a C57BL/6N mice (10- to 12-week-old males) were treated daily starting at the day of SHAM or IRI surgery (d0) with JQ1 (50 mg/kg BW) or vehicle (DMSO/10% ß-cyclo dextrin 1:10). b Serum creatinine (mg/dL) values in SHAM and IRI animals with vehicle or JQ1 at day 1 after surgery are shown (individual data points and mean ± SD). SHAM: n = 4; IRI: n = 12 biologically independent samples. c Survival curves after IRI surgery (ischemic time was 26 min at 37 °C). JQ1 treatment leads to 80% mortality after IRI surgery. Table shows number of animals alive at indicated days. d Experimental design of delayed treatment with JQ1 (50 mg/kg BW) after IRI starting at day 1, day 2, day 3 or day 4. e Serum creatinine levels at day 1 after IRI, verifying that AKI was induced to a roughly equivalent extent in each of the groups of animals that were subsequently treated with JQ1 (individual data points and mean ± SD). IRI veh: n = 11; IRI d1: n = 12; IRI d2: n = 8; IRI d3: n = 9; IRI d4: n = 7 biologically independent samples. f Survival curve after delayed JQ1 treatment starting day 1, day 2, day 3 or day 4. Table indicates number of animals alive at each day. Box indicates start of vehicle or JQ1 treatment. Source data are provided as a file.

Article Snippet: The BET inhibitor JQ1 or vehicle was provided to us by Dr. Jay Bradner (formerly at Brigham and Women’s Hospital now at the Novartis Institutes for Biomedical Research).

Techniques:

Journal: Nature Communications

Article Title: Enhancer and super-enhancer dynamics in repair after ischemic acute kidney injury

doi: 10.1038/s41467-020-17205-5

Figure Lengend Snippet: a Principal component (PC) analysis of normalized RNA-seq data matrix of SHAM, IRI and IRI JQ1 kidney cortex samples on day 2 after IRI. b Serum creatinine values at days 0, 1, and 2 after IRI comparing SHAM, IRI and IRI JQ1-treated groups. c Genes significantly differentially regulated between SHAM and IRI are shown in a heatmap of SHAM, IRI, and IRI JQ1; JQ1 leads to suppression of ~40% upregulated genes after injury. d Comparison of significantly upregulated genes 2 days after injury (SHAM vs. IRI up) and significantly down-regulated genes after JQ1 treatment (IRI vs IRI JQ1 down) with an overlap of 718 transcripts (Chi-square test P < 0.001) shown in a Venn diagram. e KEGG pathways enriched for the 718 genes upregulated after injury and down-regulated by JQ1. f Top 30 upregulated genes after injury shown in a heatmap of SHAM, IRI and IRI JQ1 samples. g Representative KIM-1/Ki67-immunostained IRI kidney cortex treated with vehicle or JQ1 at day 2 after injury, Quantification of Ki67+ cells (Ki67+ cells/total number of cells (DAPI)) and KIM-1+ surface area per hpf ( n = 4, 7 high power fields (hpf) per sample). Scale bar: 50 μm. h Fold change of Mki67 and KIM-1 after IRI comparing vehicle and JQ1 treated animals at day 2 after injury (vehicle: n = 4, JQ1: n = 6). i Genome-wide assessment of Pol II binding: Genome-wide coverage blots of Pol II on the gene body. Pol II binding after JQ1 treatment is increased at the TSS and decreased across the gene body indicating Pol II pausing j Pol II ChIP-seq tracks at the Spp1 gene body. k Fold change of Spp1 after IRI comparing vehicle and JQ1 treated animals at day 2 after injury. n = 4. Data represent the mean ± min, max. Box contains 50% of the data. t -test (two-sided) ( g , h , k ). Source data are provided as a file.

Article Snippet: The BET inhibitor JQ1 or vehicle was provided to us by Dr. Jay Bradner (formerly at Brigham and Women’s Hospital now at the Novartis Institutes for Biomedical Research).

Techniques: RNA Sequencing, Comparison, Genome Wide, Binding Assay, ChIP-sequencing

Journal: Nature Communications

Article Title: Enhancer and super-enhancer dynamics in repair after ischemic acute kidney injury

doi: 10.1038/s41467-020-17205-5

Figure Lengend Snippet: a BALB/c mice (10- to 12-week-old males) were treated daily with JQ1 (50 mg/kg) or vehicle (DMSO/10% ß-cyclo dextrin 1:10) starting on the day of aristolochic acid (AA) injection (3 mg/kg BW) or day 7 after AA injection. Mice were sacrificed on day 21 after AA injection. b Serum creatinine (mg/dL) trajectories of vehicle and JQ1 treated mice from day 0 until day 21 after AA (mean ± SD). vehicle: n = 7; JQ1 d0: n = 6; JQ1 d7: n = 8 biologically independent samples. c Survival curves after AA injection: 100% survial in vehicle and JQ1 d7 group, 67% survival in mice treated with JQ1 from day 0 until day 21 after AA injection. d Representative Ki67-1/Acta2-immunostained AAN kidneys treated with vehicle or JQ1 d0 or JQ1 d7. e Quantification of α-SMA+ (Acta2) surface area. Percentage of Ki67+ cells (Ki67+ cells/total number of cells (DAPI) per hpf). vehicle: n = 7 (60 hpf); JQ1 d0: n = 4 (33 hpf); JQ1 d7: n = 8 (64 hpf) at least 8 hpf per sample. f C57BL/6N mice (8- to 10-week-old males) were treated daily starting at the day of UUO surgery with JQ1 (50 mg/kg) or vehicle, and were sacrificed on day 10 after surgery. g Representative trichrome-stained and Sirius-red stained sections. h Quantification of fibrotic area (masson trichrome +-stained) ( n = 7, 5 hpf per sample) and Sirius red+ area (collagen) ( n = 7, at least 7 hpf per sample. t -test (two-sided). Data represent the mean ± min, max. Box contains 50% of the data. Scale bars: 100 µm ( d ), 50 μm ( g ). Source data are provided as a file.

Article Snippet: The BET inhibitor JQ1 or vehicle was provided to us by Dr. Jay Bradner (formerly at Brigham and Women’s Hospital now at the Novartis Institutes for Biomedical Research).

Techniques: Injection, Staining

Journal: Clinical and Experimental Medicine

Article Title: The epigenetic revolution in hematology: from benchside breakthroughs to clinical transformations

doi: 10.1007/s10238-025-01783-z

Figure Lengend Snippet: Summarizes the main types of epigenetic modifications along with their subtypes, associated enzymes, and their roles in gene expression regulation and hematological malignancies . Abbreviation: DNMTs: DNA methyltransferases; KMTs: Lysine methyltransferases; NSD: Nuclear SET domain; PRMTs: Protein arginine methyltransferases; CBP: CREB-binding protein; MBD: methyl-CpG-binding domain proteins; ZBTB: Zinc finger and BTB domain; BET: Bromodomain (BRD) and extra-terminal; IDH: Isocitrate dehydrogenase; KDMs: Lysine demethylases; AID/APOBEC: Activation-induced cytidine deaminase/apolipoprotein B mRNA-editing enzyme complex; HDAC: Histone deacetylase; MOZ: Monocytic leukemic zinc finger; MORF: Monocytic leukemia zinc-finger protein-related factor; TET: Ten-eleven translocation; BL: Burkitt’s lymphoma; DLBCL: Diffuse large B-cell lymphoma; NHL: Non-Hodgkin lymphoma; AML: Acute myeloid leukemia; ALL: Acute lymphoblastic leukemia; CML: Chronic myeloid leukemia; CLL: Chronic lymphocytic leukemia; MCL: Mantle cell lymphoma; MM: Multiple Myeloma; FL: Follicular lymphoma; APL: Acute promyelocytic leukemia; MDS: Myelodysplastic syndromes; PTCL: Peripheral T-cell lymphoma; CTCL: Cutaneous T-cell lymphoma; CMML: Chronic myelomonocytic leukemia; MPN: Myeloproliferative neoplasms; NKTCL: NK/T-cell lymphoma; ALCL: Anaplastic large cell lymphoma; MLL: Mixed lineage leukemia; ATLL: Adult T-cell leukemia/lymphoma; LGL: Large Granular Lymphocyte; AITL: Angioimmunoblastic T-cell lymphoma; ALAL: Acute Leukemia Of Ambiguous Lineage; AMKL: Acute Megakaryoblastic Leukemia.

Article Snippet: Other innovative therapies, including Enhancer of zeste homologue 2 (EZH2) inhibitors and Bromodomain and extra-terminal proteins (BET) inhibitors, are also being studied for their potential to target specific epigenetic alterations associated with hematological malignancies [ ].

Techniques: Gene Expression, Binding Assay, Activation Assay, Histone Deacetylase Assay, Translocation Assay