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usp7 inhibitor p22077  (MedChemExpress)


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    Structured Review

    MedChemExpress usp7 inhibitor p22077
    IP and IB analyses were performed with indicated antibodies. Data are representative of at least three independent experiments. (A) HEK293T cells were transfected with SFB-PFKM and <t>HA-USP7.</t> The cells were treated with or without GD for 6h and then Co-IP experiment was performed with anti-Flag antibody. (B) HEK293T cells were infected with the lentivirus expressing shNT or shUSP7 and then transfected with HA-Ub and SFB-PFKM. The cells were treated with or without GD for 6h and then Co-IP experiment was performed with anti-Flag antibody. (C) PFKM-depleted U87 cells reconstituted with rPFKM WT or K615R were infected with the lentivirus expressing shNT or shUSP7. Cells were treated with GD for 6h. Cytosolic (Cyto) and nuclear (Nuc) fractions were prepared. (D) PFKM-depleted U87 cells reconstituted with rPFKM WT or K615R were infected with the lentivirus expressing shNT or shUSP7. Cells were treated with GD for 48 h. Cell viability was determined using trypan blue staining. Data represent the mean ± SD of the viability of the cells from three independent experiments (two-tailed Student t test). (E–G) U87/EGFRvIII cells-depleted of endogenous PFKM and reconstituted with either rPFKM WT or the K615R mutant (2 × 10 5 per mouse) were intracranially injected into randomized athymic nude mice (five mice per group) and then treated with or without <t>P22077</t> (15 mg/kg/daily). Bioluminescence imaging of tumor growth were carried out. Representative real-time images were presented and the intensities of luciferase were quantified using living image software (PerkinElmer) (E, F) . Data represent the mean ± SD of luciferase intensity of five mice per group (two-tailed Student t test). Survival durations of these implanted mice were compared (Log-rank test) (G) . The data underlying this Figure can be found in and .
    Usp7 Inhibitor P22077, supplied by MedChemExpress, used in various techniques. Bioz Stars score: 95/100, based on 28 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Images

    1) Product Images from "USP7 facilitates brain tumor survival upon glucose deprivation by regulating phosphofructokinase muscle-type nuclear translocation in mice"

    Article Title: USP7 facilitates brain tumor survival upon glucose deprivation by regulating phosphofructokinase muscle-type nuclear translocation in mice

    Journal: PLOS Biology

    doi: 10.1371/journal.pbio.3003698

    IP and IB analyses were performed with indicated antibodies. Data are representative of at least three independent experiments. (A) HEK293T cells were transfected with SFB-PFKM and HA-USP7. The cells were treated with or without GD for 6h and then Co-IP experiment was performed with anti-Flag antibody. (B) HEK293T cells were infected with the lentivirus expressing shNT or shUSP7 and then transfected with HA-Ub and SFB-PFKM. The cells were treated with or without GD for 6h and then Co-IP experiment was performed with anti-Flag antibody. (C) PFKM-depleted U87 cells reconstituted with rPFKM WT or K615R were infected with the lentivirus expressing shNT or shUSP7. Cells were treated with GD for 6h. Cytosolic (Cyto) and nuclear (Nuc) fractions were prepared. (D) PFKM-depleted U87 cells reconstituted with rPFKM WT or K615R were infected with the lentivirus expressing shNT or shUSP7. Cells were treated with GD for 48 h. Cell viability was determined using trypan blue staining. Data represent the mean ± SD of the viability of the cells from three independent experiments (two-tailed Student t test). (E–G) U87/EGFRvIII cells-depleted of endogenous PFKM and reconstituted with either rPFKM WT or the K615R mutant (2 × 10 5 per mouse) were intracranially injected into randomized athymic nude mice (five mice per group) and then treated with or without P22077 (15 mg/kg/daily). Bioluminescence imaging of tumor growth were carried out. Representative real-time images were presented and the intensities of luciferase were quantified using living image software (PerkinElmer) (E, F) . Data represent the mean ± SD of luciferase intensity of five mice per group (two-tailed Student t test). Survival durations of these implanted mice were compared (Log-rank test) (G) . The data underlying this Figure can be found in and .
    Figure Legend Snippet: IP and IB analyses were performed with indicated antibodies. Data are representative of at least three independent experiments. (A) HEK293T cells were transfected with SFB-PFKM and HA-USP7. The cells were treated with or without GD for 6h and then Co-IP experiment was performed with anti-Flag antibody. (B) HEK293T cells were infected with the lentivirus expressing shNT or shUSP7 and then transfected with HA-Ub and SFB-PFKM. The cells were treated with or without GD for 6h and then Co-IP experiment was performed with anti-Flag antibody. (C) PFKM-depleted U87 cells reconstituted with rPFKM WT or K615R were infected with the lentivirus expressing shNT or shUSP7. Cells were treated with GD for 6h. Cytosolic (Cyto) and nuclear (Nuc) fractions were prepared. (D) PFKM-depleted U87 cells reconstituted with rPFKM WT or K615R were infected with the lentivirus expressing shNT or shUSP7. Cells were treated with GD for 48 h. Cell viability was determined using trypan blue staining. Data represent the mean ± SD of the viability of the cells from three independent experiments (two-tailed Student t test). (E–G) U87/EGFRvIII cells-depleted of endogenous PFKM and reconstituted with either rPFKM WT or the K615R mutant (2 × 10 5 per mouse) were intracranially injected into randomized athymic nude mice (five mice per group) and then treated with or without P22077 (15 mg/kg/daily). Bioluminescence imaging of tumor growth were carried out. Representative real-time images were presented and the intensities of luciferase were quantified using living image software (PerkinElmer) (E, F) . Data represent the mean ± SD of luciferase intensity of five mice per group (two-tailed Student t test). Survival durations of these implanted mice were compared (Log-rank test) (G) . The data underlying this Figure can be found in and .

    Techniques Used: Transfection, Co-Immunoprecipitation Assay, Infection, Expressing, Staining, Two Tailed Test, Mutagenesis, Injection, Imaging, Luciferase, Software

    (A) HEK293T cells were transfected with SFB-PFKM and HA-USP7 and then treated with GD for 6 h. SFB-PFKM is immunoprecipitated using Flag beads and the precipitate is incubated with or without F-2,6-BP/Citrate/AMP/ADP/ATP (100 μM). (B) HEK293T cells were transfected with SFB-PFKM and HA-USP7. The cells were supplemented with or without F-2,6-BP (100 μM) by electroporation and then treated with or without GD for 6 h. Co-IP experiment was performed with anti-Flag antibody. (C) HEK293T cells were transfected with SFB-PFKM and HA-Ub. The cells were supplemented with or without F-2,6-BP (100 μM) by electroporation and then treated with or without GD for 6 h. Co-IP experiment was performed with anti-Flag antibody. (D) U87 cells were treated with or without GD for 6 h. The cell lysis were collected for measurement of F-2,6-BP concentrations as determined by F-2,6-BP assay kit (Huabang Biotechnology, China). (E) HEK293T cells were transfected with SFB-PFKM and HA-USP7 and then treated with or without 3PO (20 μM, 12 h). Co-IP experiment was performed with anti-Flag antibody. (F) HEK293T cells were transfected with SFB-PFKM and HA-Ub and then treated with or without 3PO (20 μM, 12 h). Co-IP experiment was performed with anti-Flag antibody. (G) HEK293T cells were transfected with HA-USP7 and Flag-PFKM WT or F639L and then treated with GD for 6 h. Co-IP experiment was performed with anti-Flag antibody. (H) HEK293T cells were transfected with either HA-USP7 or Flag-PFKM and treated with GD for 6 h. Following this, Flag-PFKM and HA-USP7 were immunoprecipitated and purified from the respective cell lysates. For the pull-down assay, the purified Flag-PFKM was first pre-incubated with F-2,6-BP. After removing unbound F-2,6-BP through washing, it was then mixed with HA-USP7 to proceed with the pull-down assay. (I) HEK293T cells were transfected with either HA-USP7 or Flag-PFKM and treated with GD for 6 h. Following this, Flag-PFKM and HA-USP7 were immunoprecipitated and purified from the respective cell lysates. For the pull-down assay, the purified HA-USP7 was first pre-incubated with F-2,6-BP. After removing unbound F-2,6-BP through washing, it was then mixed with Flag-PFKM to proceed with the pull-down assay. The data underlying this Figure can be found in and .
    Figure Legend Snippet: (A) HEK293T cells were transfected with SFB-PFKM and HA-USP7 and then treated with GD for 6 h. SFB-PFKM is immunoprecipitated using Flag beads and the precipitate is incubated with or without F-2,6-BP/Citrate/AMP/ADP/ATP (100 μM). (B) HEK293T cells were transfected with SFB-PFKM and HA-USP7. The cells were supplemented with or without F-2,6-BP (100 μM) by electroporation and then treated with or without GD for 6 h. Co-IP experiment was performed with anti-Flag antibody. (C) HEK293T cells were transfected with SFB-PFKM and HA-Ub. The cells were supplemented with or without F-2,6-BP (100 μM) by electroporation and then treated with or without GD for 6 h. Co-IP experiment was performed with anti-Flag antibody. (D) U87 cells were treated with or without GD for 6 h. The cell lysis were collected for measurement of F-2,6-BP concentrations as determined by F-2,6-BP assay kit (Huabang Biotechnology, China). (E) HEK293T cells were transfected with SFB-PFKM and HA-USP7 and then treated with or without 3PO (20 μM, 12 h). Co-IP experiment was performed with anti-Flag antibody. (F) HEK293T cells were transfected with SFB-PFKM and HA-Ub and then treated with or without 3PO (20 μM, 12 h). Co-IP experiment was performed with anti-Flag antibody. (G) HEK293T cells were transfected with HA-USP7 and Flag-PFKM WT or F639L and then treated with GD for 6 h. Co-IP experiment was performed with anti-Flag antibody. (H) HEK293T cells were transfected with either HA-USP7 or Flag-PFKM and treated with GD for 6 h. Following this, Flag-PFKM and HA-USP7 were immunoprecipitated and purified from the respective cell lysates. For the pull-down assay, the purified Flag-PFKM was first pre-incubated with F-2,6-BP. After removing unbound F-2,6-BP through washing, it was then mixed with HA-USP7 to proceed with the pull-down assay. (I) HEK293T cells were transfected with either HA-USP7 or Flag-PFKM and treated with GD for 6 h. Following this, Flag-PFKM and HA-USP7 were immunoprecipitated and purified from the respective cell lysates. For the pull-down assay, the purified HA-USP7 was first pre-incubated with F-2,6-BP. After removing unbound F-2,6-BP through washing, it was then mixed with Flag-PFKM to proceed with the pull-down assay. The data underlying this Figure can be found in and .

    Techniques Used: Transfection, Immunoprecipitation, Incubation, Electroporation, Co-Immunoprecipitation Assay, Lysis, Purification, Pull Down Assay

    USP7 interacts with PFKM regulated by F-2,6-BP, resulting in the ubiquitination of PFKM K615 after GD treatment. Deubiquitinated PFKM translocates into nucleus and interacts with c-Myc. PFKM facilitates c-MYC binding to CPT1B promoter and promotes transcription of CPT1B, thereby enhancing FAO and cell survival.
    Figure Legend Snippet: USP7 interacts with PFKM regulated by F-2,6-BP, resulting in the ubiquitination of PFKM K615 after GD treatment. Deubiquitinated PFKM translocates into nucleus and interacts with c-Myc. PFKM facilitates c-MYC binding to CPT1B promoter and promotes transcription of CPT1B, thereby enhancing FAO and cell survival.

    Techniques Used: Ubiquitin Proteomics, Binding Assay



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    IP and IB analyses were performed with indicated antibodies. Data are representative of at least three independent experiments. (A) HEK293T cells were transfected with SFB-PFKM and <t>HA-USP7.</t> The cells were treated with or without GD for 6h and then Co-IP experiment was performed with anti-Flag antibody. (B) HEK293T cells were infected with the lentivirus expressing shNT or shUSP7 and then transfected with HA-Ub and SFB-PFKM. The cells were treated with or without GD for 6h and then Co-IP experiment was performed with anti-Flag antibody. (C) PFKM-depleted U87 cells reconstituted with rPFKM WT or K615R were infected with the lentivirus expressing shNT or shUSP7. Cells were treated with GD for 6h. Cytosolic (Cyto) and nuclear (Nuc) fractions were prepared. (D) PFKM-depleted U87 cells reconstituted with rPFKM WT or K615R were infected with the lentivirus expressing shNT or shUSP7. Cells were treated with GD for 48 h. Cell viability was determined using trypan blue staining. Data represent the mean ± SD of the viability of the cells from three independent experiments (two-tailed Student t test). (E–G) U87/EGFRvIII cells-depleted of endogenous PFKM and reconstituted with either rPFKM WT or the K615R mutant (2 × 10 5 per mouse) were intracranially injected into randomized athymic nude mice (five mice per group) and then treated with or without <t>P22077</t> (15 mg/kg/daily). Bioluminescence imaging of tumor growth were carried out. Representative real-time images were presented and the intensities of luciferase were quantified using living image software (PerkinElmer) (E, F) . Data represent the mean ± SD of luciferase intensity of five mice per group (two-tailed Student t test). Survival durations of these implanted mice were compared (Log-rank test) (G) . The data underlying this Figure can be found in and .
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    Selleck Chemicals usp7 inhibitor p22077
    IP and IB analyses were performed with indicated antibodies. Data are representative of at least three independent experiments. (A) HEK293T cells were transfected with SFB-PFKM and <t>HA-USP7.</t> The cells were treated with or without GD for 6h and then Co-IP experiment was performed with anti-Flag antibody. (B) HEK293T cells were infected with the lentivirus expressing shNT or shUSP7 and then transfected with HA-Ub and SFB-PFKM. The cells were treated with or without GD for 6h and then Co-IP experiment was performed with anti-Flag antibody. (C) PFKM-depleted U87 cells reconstituted with rPFKM WT or K615R were infected with the lentivirus expressing shNT or shUSP7. Cells were treated with GD for 6h. Cytosolic (Cyto) and nuclear (Nuc) fractions were prepared. (D) PFKM-depleted U87 cells reconstituted with rPFKM WT or K615R were infected with the lentivirus expressing shNT or shUSP7. Cells were treated with GD for 48 h. Cell viability was determined using trypan blue staining. Data represent the mean ± SD of the viability of the cells from three independent experiments (two-tailed Student t test). (E–G) U87/EGFRvIII cells-depleted of endogenous PFKM and reconstituted with either rPFKM WT or the K615R mutant (2 × 10 5 per mouse) were intracranially injected into randomized athymic nude mice (five mice per group) and then treated with or without <t>P22077</t> (15 mg/kg/daily). Bioluminescence imaging of tumor growth were carried out. Representative real-time images were presented and the intensities of luciferase were quantified using living image software (PerkinElmer) (E, F) . Data represent the mean ± SD of luciferase intensity of five mice per group (two-tailed Student t test). Survival durations of these implanted mice were compared (Log-rank test) (G) . The data underlying this Figure can be found in and .
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    Fig. 1. Screening of putative substrates using [P/A/E]-X-X-S and K-X-X-K motifs. (A-C) Gene ontology (GO) analysis of putative substrates for ubiquitin-specific proteases 7 <t>(USP7)</t> was performed by the database for annotation, visualization, and integrated discovery (DAVID) analysis. Y-axis indicates the GO terms and X-axis indicates gene count in the GO terms. The asterisk means the p-value (* p < 0.05, ** p < 0.01, *** p < 0.001.) (D-E) Protein-protein interaction network of transcription factors and USP7 was shown by Cytoscape. The color of nodes indicates connection to the node of USP7 (Blue: USP7, Red: connection, Gray: no connection). *Abbreviation: GO: Gene ontology; DAVID: the database for annotation, visualization, and integrated discovery; USP7: ubiquitin-specific proteases 7.
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    Fig. 1. Screening of putative substrates using [P/A/E]-X-X-S and K-X-X-K motifs. (A-C) Gene ontology (GO) analysis of putative substrates for ubiquitin-specific proteases 7 <t>(USP7)</t> was performed by the database for annotation, visualization, and integrated discovery (DAVID) analysis. Y-axis indicates the GO terms and X-axis indicates gene count in the GO terms. The asterisk means the p-value (* p < 0.05, ** p < 0.01, *** p < 0.001.) (D-E) Protein-protein interaction network of transcription factors and USP7 was shown by Cytoscape. The color of nodes indicates connection to the node of USP7 (Blue: USP7, Red: connection, Gray: no connection). *Abbreviation: GO: Gene ontology; DAVID: the database for annotation, visualization, and integrated discovery; USP7: ubiquitin-specific proteases 7.
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    LC-MS/MS-based identification of new PRC1.1 subunits (A) LC-MS/MS analysis of KDM2B-GFP, GFP-RING1B, and PCGF1-GFP pull outs in K562 cells showing 20 overlapping interaction partners including PRC1.1 subunits (in red) and new interaction partners such as <t>USP7</t> and TRIM27 (in blue). (B) Schematic overview of PRC1.1 subunit composition. PRC1.1 preferentially binds to non-methylated CpG islands via the CxxC domain of KDM2B. The ubiquitination of histone H2A on lysine 119 is mediated by RING1A/B. (C) Schematic representation of KDM2B deletion mutants and the endogenously expressed long form (LF) and short form (SF; lacking the JmjC domain) of KDM2B. (D) Western blots showing expression of GFP-fusions at near to endogenous KDM2B expression levels. (E) Table showing LC-MS/MS data of PRC1.1 subunits and other PcG proteins co-precipitating with wild-type and mutant forms of KDM2B-GFP. Numbers indicate the average total spectra counts, as measured in triplicate, corrected for maximally identifiable peptides based on in silico protein digests. (F) Volcano plot showing MaxQuant-based label-free quantification of triplicate measurements of KDM2B LF-GFP and KDM2B Δ(LRR)-GFP pull outs. PRC1.1 subunits are indicated in red and USP7 and TRIM27 in blue. (G) Western blot analysis of independent pull outs of (mutant) KDM2B-GFP with input (I, 1/90 th ), non-bound (NB, 1/90 th ), and bound (B, 1/3 rd ) fractions loaded and stained with antibodies against GFP, PCGF1, RING1B, USP7, and TRIM27. (H) PCGF1-GFP pull outs with input (I, 1/90 th ), non-bound (NB, 1/90 th ), and bound (B, 1/3 rd ) and stained with antibodies directed against GFP, KDM2B, RING1B, USP7, and TRIM27. See also <xref ref-type=Figure S1 and , , and . " width="250" height="auto" />
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    LC-MS/MS-based identification of new PRC1.1 subunits (A) LC-MS/MS analysis of KDM2B-GFP, GFP-RING1B, and PCGF1-GFP pull outs in K562 cells showing 20 overlapping interaction partners including PRC1.1 subunits (in red) and new interaction partners such as <t>USP7</t> and TRIM27 (in blue). (B) Schematic overview of PRC1.1 subunit composition. PRC1.1 preferentially binds to non-methylated CpG islands via the CxxC domain of KDM2B. The ubiquitination of histone H2A on lysine 119 is mediated by RING1A/B. (C) Schematic representation of KDM2B deletion mutants and the endogenously expressed long form (LF) and short form (SF; lacking the JmjC domain) of KDM2B. (D) Western blots showing expression of GFP-fusions at near to endogenous KDM2B expression levels. (E) Table showing LC-MS/MS data of PRC1.1 subunits and other PcG proteins co-precipitating with wild-type and mutant forms of KDM2B-GFP. Numbers indicate the average total spectra counts, as measured in triplicate, corrected for maximally identifiable peptides based on in silico protein digests. (F) Volcano plot showing MaxQuant-based label-free quantification of triplicate measurements of KDM2B LF-GFP and KDM2B Δ(LRR)-GFP pull outs. PRC1.1 subunits are indicated in red and USP7 and TRIM27 in blue. (G) Western blot analysis of independent pull outs of (mutant) KDM2B-GFP with input (I, 1/90 th ), non-bound (NB, 1/90 th ), and bound (B, 1/3 rd ) fractions loaded and stained with antibodies against GFP, PCGF1, RING1B, USP7, and TRIM27. (H) PCGF1-GFP pull outs with input (I, 1/90 th ), non-bound (NB, 1/90 th ), and bound (B, 1/3 rd ) and stained with antibodies directed against GFP, KDM2B, RING1B, USP7, and TRIM27. See also <xref ref-type=Figure S1 and , , and . " width="250" height="auto" />
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    IP and IB analyses were performed with indicated antibodies. Data are representative of at least three independent experiments. (A) HEK293T cells were transfected with SFB-PFKM and HA-USP7. The cells were treated with or without GD for 6h and then Co-IP experiment was performed with anti-Flag antibody. (B) HEK293T cells were infected with the lentivirus expressing shNT or shUSP7 and then transfected with HA-Ub and SFB-PFKM. The cells were treated with or without GD for 6h and then Co-IP experiment was performed with anti-Flag antibody. (C) PFKM-depleted U87 cells reconstituted with rPFKM WT or K615R were infected with the lentivirus expressing shNT or shUSP7. Cells were treated with GD for 6h. Cytosolic (Cyto) and nuclear (Nuc) fractions were prepared. (D) PFKM-depleted U87 cells reconstituted with rPFKM WT or K615R were infected with the lentivirus expressing shNT or shUSP7. Cells were treated with GD for 48 h. Cell viability was determined using trypan blue staining. Data represent the mean ± SD of the viability of the cells from three independent experiments (two-tailed Student t test). (E–G) U87/EGFRvIII cells-depleted of endogenous PFKM and reconstituted with either rPFKM WT or the K615R mutant (2 × 10 5 per mouse) were intracranially injected into randomized athymic nude mice (five mice per group) and then treated with or without P22077 (15 mg/kg/daily). Bioluminescence imaging of tumor growth were carried out. Representative real-time images were presented and the intensities of luciferase were quantified using living image software (PerkinElmer) (E, F) . Data represent the mean ± SD of luciferase intensity of five mice per group (two-tailed Student t test). Survival durations of these implanted mice were compared (Log-rank test) (G) . The data underlying this Figure can be found in and .

    Journal: PLOS Biology

    Article Title: USP7 facilitates brain tumor survival upon glucose deprivation by regulating phosphofructokinase muscle-type nuclear translocation in mice

    doi: 10.1371/journal.pbio.3003698

    Figure Lengend Snippet: IP and IB analyses were performed with indicated antibodies. Data are representative of at least three independent experiments. (A) HEK293T cells were transfected with SFB-PFKM and HA-USP7. The cells were treated with or without GD for 6h and then Co-IP experiment was performed with anti-Flag antibody. (B) HEK293T cells were infected with the lentivirus expressing shNT or shUSP7 and then transfected with HA-Ub and SFB-PFKM. The cells were treated with or without GD for 6h and then Co-IP experiment was performed with anti-Flag antibody. (C) PFKM-depleted U87 cells reconstituted with rPFKM WT or K615R were infected with the lentivirus expressing shNT or shUSP7. Cells were treated with GD for 6h. Cytosolic (Cyto) and nuclear (Nuc) fractions were prepared. (D) PFKM-depleted U87 cells reconstituted with rPFKM WT or K615R were infected with the lentivirus expressing shNT or shUSP7. Cells were treated with GD for 48 h. Cell viability was determined using trypan blue staining. Data represent the mean ± SD of the viability of the cells from three independent experiments (two-tailed Student t test). (E–G) U87/EGFRvIII cells-depleted of endogenous PFKM and reconstituted with either rPFKM WT or the K615R mutant (2 × 10 5 per mouse) were intracranially injected into randomized athymic nude mice (five mice per group) and then treated with or without P22077 (15 mg/kg/daily). Bioluminescence imaging of tumor growth were carried out. Representative real-time images were presented and the intensities of luciferase were quantified using living image software (PerkinElmer) (E, F) . Data represent the mean ± SD of luciferase intensity of five mice per group (two-tailed Student t test). Survival durations of these implanted mice were compared (Log-rank test) (G) . The data underlying this Figure can be found in and .

    Article Snippet: The PFK2 inhibitor-3PO (HY-19824), USP7 inhibitor- P22077 (HY-13865), glutaminase inhibitor BPTES (HY-12683) and FAO inhibitor Etomoxir (HY-50202) were purchased from MCE (MedChemExpress, China).

    Techniques: Transfection, Co-Immunoprecipitation Assay, Infection, Expressing, Staining, Two Tailed Test, Mutagenesis, Injection, Imaging, Luciferase, Software

    (A) HEK293T cells were transfected with SFB-PFKM and HA-USP7 and then treated with GD for 6 h. SFB-PFKM is immunoprecipitated using Flag beads and the precipitate is incubated with or without F-2,6-BP/Citrate/AMP/ADP/ATP (100 μM). (B) HEK293T cells were transfected with SFB-PFKM and HA-USP7. The cells were supplemented with or without F-2,6-BP (100 μM) by electroporation and then treated with or without GD for 6 h. Co-IP experiment was performed with anti-Flag antibody. (C) HEK293T cells were transfected with SFB-PFKM and HA-Ub. The cells were supplemented with or without F-2,6-BP (100 μM) by electroporation and then treated with or without GD for 6 h. Co-IP experiment was performed with anti-Flag antibody. (D) U87 cells were treated with or without GD for 6 h. The cell lysis were collected for measurement of F-2,6-BP concentrations as determined by F-2,6-BP assay kit (Huabang Biotechnology, China). (E) HEK293T cells were transfected with SFB-PFKM and HA-USP7 and then treated with or without 3PO (20 μM, 12 h). Co-IP experiment was performed with anti-Flag antibody. (F) HEK293T cells were transfected with SFB-PFKM and HA-Ub and then treated with or without 3PO (20 μM, 12 h). Co-IP experiment was performed with anti-Flag antibody. (G) HEK293T cells were transfected with HA-USP7 and Flag-PFKM WT or F639L and then treated with GD for 6 h. Co-IP experiment was performed with anti-Flag antibody. (H) HEK293T cells were transfected with either HA-USP7 or Flag-PFKM and treated with GD for 6 h. Following this, Flag-PFKM and HA-USP7 were immunoprecipitated and purified from the respective cell lysates. For the pull-down assay, the purified Flag-PFKM was first pre-incubated with F-2,6-BP. After removing unbound F-2,6-BP through washing, it was then mixed with HA-USP7 to proceed with the pull-down assay. (I) HEK293T cells were transfected with either HA-USP7 or Flag-PFKM and treated with GD for 6 h. Following this, Flag-PFKM and HA-USP7 were immunoprecipitated and purified from the respective cell lysates. For the pull-down assay, the purified HA-USP7 was first pre-incubated with F-2,6-BP. After removing unbound F-2,6-BP through washing, it was then mixed with Flag-PFKM to proceed with the pull-down assay. The data underlying this Figure can be found in and .

    Journal: PLOS Biology

    Article Title: USP7 facilitates brain tumor survival upon glucose deprivation by regulating phosphofructokinase muscle-type nuclear translocation in mice

    doi: 10.1371/journal.pbio.3003698

    Figure Lengend Snippet: (A) HEK293T cells were transfected with SFB-PFKM and HA-USP7 and then treated with GD for 6 h. SFB-PFKM is immunoprecipitated using Flag beads and the precipitate is incubated with or without F-2,6-BP/Citrate/AMP/ADP/ATP (100 μM). (B) HEK293T cells were transfected with SFB-PFKM and HA-USP7. The cells were supplemented with or without F-2,6-BP (100 μM) by electroporation and then treated with or without GD for 6 h. Co-IP experiment was performed with anti-Flag antibody. (C) HEK293T cells were transfected with SFB-PFKM and HA-Ub. The cells were supplemented with or without F-2,6-BP (100 μM) by electroporation and then treated with or without GD for 6 h. Co-IP experiment was performed with anti-Flag antibody. (D) U87 cells were treated with or without GD for 6 h. The cell lysis were collected for measurement of F-2,6-BP concentrations as determined by F-2,6-BP assay kit (Huabang Biotechnology, China). (E) HEK293T cells were transfected with SFB-PFKM and HA-USP7 and then treated with or without 3PO (20 μM, 12 h). Co-IP experiment was performed with anti-Flag antibody. (F) HEK293T cells were transfected with SFB-PFKM and HA-Ub and then treated with or without 3PO (20 μM, 12 h). Co-IP experiment was performed with anti-Flag antibody. (G) HEK293T cells were transfected with HA-USP7 and Flag-PFKM WT or F639L and then treated with GD for 6 h. Co-IP experiment was performed with anti-Flag antibody. (H) HEK293T cells were transfected with either HA-USP7 or Flag-PFKM and treated with GD for 6 h. Following this, Flag-PFKM and HA-USP7 were immunoprecipitated and purified from the respective cell lysates. For the pull-down assay, the purified Flag-PFKM was first pre-incubated with F-2,6-BP. After removing unbound F-2,6-BP through washing, it was then mixed with HA-USP7 to proceed with the pull-down assay. (I) HEK293T cells were transfected with either HA-USP7 or Flag-PFKM and treated with GD for 6 h. Following this, Flag-PFKM and HA-USP7 were immunoprecipitated and purified from the respective cell lysates. For the pull-down assay, the purified HA-USP7 was first pre-incubated with F-2,6-BP. After removing unbound F-2,6-BP through washing, it was then mixed with Flag-PFKM to proceed with the pull-down assay. The data underlying this Figure can be found in and .

    Article Snippet: The PFK2 inhibitor-3PO (HY-19824), USP7 inhibitor- P22077 (HY-13865), glutaminase inhibitor BPTES (HY-12683) and FAO inhibitor Etomoxir (HY-50202) were purchased from MCE (MedChemExpress, China).

    Techniques: Transfection, Immunoprecipitation, Incubation, Electroporation, Co-Immunoprecipitation Assay, Lysis, Purification, Pull Down Assay

    USP7 interacts with PFKM regulated by F-2,6-BP, resulting in the ubiquitination of PFKM K615 after GD treatment. Deubiquitinated PFKM translocates into nucleus and interacts with c-Myc. PFKM facilitates c-MYC binding to CPT1B promoter and promotes transcription of CPT1B, thereby enhancing FAO and cell survival.

    Journal: PLOS Biology

    Article Title: USP7 facilitates brain tumor survival upon glucose deprivation by regulating phosphofructokinase muscle-type nuclear translocation in mice

    doi: 10.1371/journal.pbio.3003698

    Figure Lengend Snippet: USP7 interacts with PFKM regulated by F-2,6-BP, resulting in the ubiquitination of PFKM K615 after GD treatment. Deubiquitinated PFKM translocates into nucleus and interacts with c-Myc. PFKM facilitates c-MYC binding to CPT1B promoter and promotes transcription of CPT1B, thereby enhancing FAO and cell survival.

    Article Snippet: The PFK2 inhibitor-3PO (HY-19824), USP7 inhibitor- P22077 (HY-13865), glutaminase inhibitor BPTES (HY-12683) and FAO inhibitor Etomoxir (HY-50202) were purchased from MCE (MedChemExpress, China).

    Techniques: Ubiquitin Proteomics, Binding Assay

    Fig. 1. Screening of putative substrates using [P/A/E]-X-X-S and K-X-X-K motifs. (A-C) Gene ontology (GO) analysis of putative substrates for ubiquitin-specific proteases 7 (USP7) was performed by the database for annotation, visualization, and integrated discovery (DAVID) analysis. Y-axis indicates the GO terms and X-axis indicates gene count in the GO terms. The asterisk means the p-value (* p < 0.05, ** p < 0.01, *** p < 0.001.) (D-E) Protein-protein interaction network of transcription factors and USP7 was shown by Cytoscape. The color of nodes indicates connection to the node of USP7 (Blue: USP7, Red: connection, Gray: no connection). *Abbreviation: GO: Gene ontology; DAVID: the database for annotation, visualization, and integrated discovery; USP7: ubiquitin-specific proteases 7.

    Journal: Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie

    Article Title: Suppression of USP7 negatively regulates the stability of ETS proto-oncogene 2 protein.

    doi: 10.1016/j.biopha.2023.114700

    Figure Lengend Snippet: Fig. 1. Screening of putative substrates using [P/A/E]-X-X-S and K-X-X-K motifs. (A-C) Gene ontology (GO) analysis of putative substrates for ubiquitin-specific proteases 7 (USP7) was performed by the database for annotation, visualization, and integrated discovery (DAVID) analysis. Y-axis indicates the GO terms and X-axis indicates gene count in the GO terms. The asterisk means the p-value (* p < 0.05, ** p < 0.01, *** p < 0.001.) (D-E) Protein-protein interaction network of transcription factors and USP7 was shown by Cytoscape. The color of nodes indicates connection to the node of USP7 (Blue: USP7, Red: connection, Gray: no connection). *Abbreviation: GO: Gene ontology; DAVID: the database for annotation, visualization, and integrated discovery; USP7: ubiquitin-specific proteases 7.

    Article Snippet: And pGL3-basic vector or pGL3-EBS was transfected with siUSP7 or USP7 inhibitors (P22077 or P5091 (Cat #S7132, Selleck Chemicals, TX, USA)) in HeLa cells.

    Techniques: Ubiquitin Proteomics

    Fig. 2. USP7 binds to ETS2, but not ETS1. (A-B) HEK293T cell lysates were precipitated by an anti-ubiquitin-specific proteases 7 (USP7) antibody, and binding between USP7 and ETS proto-oncogene 1 (ETS1), and between USP7 and ETS proto-oncogene 2 (ETS2) was confirmed by immunoprecipitation assay. (C) HeLa cell lysates were precipitated by an anti-USP7 antibody, and binding between USP7 and ETS2 was confirmed by immunoprecipitation assay. (D) Myc-USP7 and ETS2-Flag were co-transfected into HEK293T cells, and binding between Myc-USP7 and ETS2-Flag was confirmed using an anti-Myc or an anti-Flag antibody. (E) GST pull-down assay was performed using purified GST or GST-USP7 from BL21 and ETS2-Flag-transfected HEK293T cells. Direct binding between GST-USP7 and ETS2-Flag was checked by Western blotting and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) gel was stained by Coomassie Brilliant Blue. (F) Co- localization between USP7 and ETS2 was confirmed by immunocytochemical analysis in HeLa and HEK293T cells (Red: USP7, Green: ETS2, and Blue: nucleus). *Abbreviation: USP7: ubiquitin-specific proteases 7; ETS1: ETS proto-oncogene 1; ETS2: ETS proto-oncogene 2; GO: Gene ontology; SDS-PAGE: sodium dodecyl sulfate polyacrylamide gel electrophoresis.

    Journal: Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie

    Article Title: Suppression of USP7 negatively regulates the stability of ETS proto-oncogene 2 protein.

    doi: 10.1016/j.biopha.2023.114700

    Figure Lengend Snippet: Fig. 2. USP7 binds to ETS2, but not ETS1. (A-B) HEK293T cell lysates were precipitated by an anti-ubiquitin-specific proteases 7 (USP7) antibody, and binding between USP7 and ETS proto-oncogene 1 (ETS1), and between USP7 and ETS proto-oncogene 2 (ETS2) was confirmed by immunoprecipitation assay. (C) HeLa cell lysates were precipitated by an anti-USP7 antibody, and binding between USP7 and ETS2 was confirmed by immunoprecipitation assay. (D) Myc-USP7 and ETS2-Flag were co-transfected into HEK293T cells, and binding between Myc-USP7 and ETS2-Flag was confirmed using an anti-Myc or an anti-Flag antibody. (E) GST pull-down assay was performed using purified GST or GST-USP7 from BL21 and ETS2-Flag-transfected HEK293T cells. Direct binding between GST-USP7 and ETS2-Flag was checked by Western blotting and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) gel was stained by Coomassie Brilliant Blue. (F) Co- localization between USP7 and ETS2 was confirmed by immunocytochemical analysis in HeLa and HEK293T cells (Red: USP7, Green: ETS2, and Blue: nucleus). *Abbreviation: USP7: ubiquitin-specific proteases 7; ETS1: ETS proto-oncogene 1; ETS2: ETS proto-oncogene 2; GO: Gene ontology; SDS-PAGE: sodium dodecyl sulfate polyacrylamide gel electrophoresis.

    Article Snippet: And pGL3-basic vector or pGL3-EBS was transfected with siUSP7 or USP7 inhibitors (P22077 or P5091 (Cat #S7132, Selleck Chemicals, TX, USA)) in HeLa cells.

    Techniques: Ubiquitin Proteomics, Binding Assay, Immunoprecipitation, Transfection, Pull Down Assay, Purification, Western Blot, Polyacrylamide Gel Electrophoresis, SDS Page, Staining

    Fig. 3. TRAF domain of USP7 binds to the AVMS motif of ETS2. (A-B) The deletion mutants of USP7 are shown by the schematic drawing (USP7 (TRAF): tumor necrosis factor receptor–associated factor (TRAF) domain of USP7 and USP7 (UBL): ubiquitin-like (UBL) domain). ETS2-Flag and deletion mutants of Myc-USP7 were co-transfected into HEK293T cells, and the binding domain of USP7 was identified by immunoprecipitation assay. (C-D) [P/A/E]-X-X-S motifs of ETS2 were shown by the schematic drawing and these motifs were mutated to identify the binding motif of ETS2. 6 [P/A/E]-X-X-S motif mutants of ETS2 and Myc-USP7 were co- transfected in HEK293T cells, and a binding motif of ETS2 was confirmed by immunoprecipitation assay. *Abbreviation: TRAF: tumor necrosis factor recep tor–associated factor; UBL: ubiquitin-like.

    Journal: Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie

    Article Title: Suppression of USP7 negatively regulates the stability of ETS proto-oncogene 2 protein.

    doi: 10.1016/j.biopha.2023.114700

    Figure Lengend Snippet: Fig. 3. TRAF domain of USP7 binds to the AVMS motif of ETS2. (A-B) The deletion mutants of USP7 are shown by the schematic drawing (USP7 (TRAF): tumor necrosis factor receptor–associated factor (TRAF) domain of USP7 and USP7 (UBL): ubiquitin-like (UBL) domain). ETS2-Flag and deletion mutants of Myc-USP7 were co-transfected into HEK293T cells, and the binding domain of USP7 was identified by immunoprecipitation assay. (C-D) [P/A/E]-X-X-S motifs of ETS2 were shown by the schematic drawing and these motifs were mutated to identify the binding motif of ETS2. 6 [P/A/E]-X-X-S motif mutants of ETS2 and Myc-USP7 were co- transfected in HEK293T cells, and a binding motif of ETS2 was confirmed by immunoprecipitation assay. *Abbreviation: TRAF: tumor necrosis factor recep tor–associated factor; UBL: ubiquitin-like.

    Article Snippet: And pGL3-basic vector or pGL3-EBS was transfected with siUSP7 or USP7 inhibitors (P22077 or P5091 (Cat #S7132, Selleck Chemicals, TX, USA)) in HeLa cells.

    Techniques: Ubiquitin Proteomics, Transfection, Binding Assay, Immunoprecipitation

    LC-MS/MS-based identification of new PRC1.1 subunits (A) LC-MS/MS analysis of KDM2B-GFP, GFP-RING1B, and PCGF1-GFP pull outs in K562 cells showing 20 overlapping interaction partners including PRC1.1 subunits (in red) and new interaction partners such as USP7 and TRIM27 (in blue). (B) Schematic overview of PRC1.1 subunit composition. PRC1.1 preferentially binds to non-methylated CpG islands via the CxxC domain of KDM2B. The ubiquitination of histone H2A on lysine 119 is mediated by RING1A/B. (C) Schematic representation of KDM2B deletion mutants and the endogenously expressed long form (LF) and short form (SF; lacking the JmjC domain) of KDM2B. (D) Western blots showing expression of GFP-fusions at near to endogenous KDM2B expression levels. (E) Table showing LC-MS/MS data of PRC1.1 subunits and other PcG proteins co-precipitating with wild-type and mutant forms of KDM2B-GFP. Numbers indicate the average total spectra counts, as measured in triplicate, corrected for maximally identifiable peptides based on in silico protein digests. (F) Volcano plot showing MaxQuant-based label-free quantification of triplicate measurements of KDM2B LF-GFP and KDM2B Δ(LRR)-GFP pull outs. PRC1.1 subunits are indicated in red and USP7 and TRIM27 in blue. (G) Western blot analysis of independent pull outs of (mutant) KDM2B-GFP with input (I, 1/90 th ), non-bound (NB, 1/90 th ), and bound (B, 1/3 rd ) fractions loaded and stained with antibodies against GFP, PCGF1, RING1B, USP7, and TRIM27. (H) PCGF1-GFP pull outs with input (I, 1/90 th ), non-bound (NB, 1/90 th ), and bound (B, 1/3 rd ) and stained with antibodies directed against GFP, KDM2B, RING1B, USP7, and TRIM27. See also <xref ref-type=Figure S1 and , , and . " width="100%" height="100%">

    Journal: iScience

    Article Title: The USP7-TRIM27 axis mediates non-canonical PRC1.1 function and is a druggable target in leukemia

    doi: 10.1016/j.isci.2021.102435

    Figure Lengend Snippet: LC-MS/MS-based identification of new PRC1.1 subunits (A) LC-MS/MS analysis of KDM2B-GFP, GFP-RING1B, and PCGF1-GFP pull outs in K562 cells showing 20 overlapping interaction partners including PRC1.1 subunits (in red) and new interaction partners such as USP7 and TRIM27 (in blue). (B) Schematic overview of PRC1.1 subunit composition. PRC1.1 preferentially binds to non-methylated CpG islands via the CxxC domain of KDM2B. The ubiquitination of histone H2A on lysine 119 is mediated by RING1A/B. (C) Schematic representation of KDM2B deletion mutants and the endogenously expressed long form (LF) and short form (SF; lacking the JmjC domain) of KDM2B. (D) Western blots showing expression of GFP-fusions at near to endogenous KDM2B expression levels. (E) Table showing LC-MS/MS data of PRC1.1 subunits and other PcG proteins co-precipitating with wild-type and mutant forms of KDM2B-GFP. Numbers indicate the average total spectra counts, as measured in triplicate, corrected for maximally identifiable peptides based on in silico protein digests. (F) Volcano plot showing MaxQuant-based label-free quantification of triplicate measurements of KDM2B LF-GFP and KDM2B Δ(LRR)-GFP pull outs. PRC1.1 subunits are indicated in red and USP7 and TRIM27 in blue. (G) Western blot analysis of independent pull outs of (mutant) KDM2B-GFP with input (I, 1/90 th ), non-bound (NB, 1/90 th ), and bound (B, 1/3 rd ) fractions loaded and stained with antibodies against GFP, PCGF1, RING1B, USP7, and TRIM27. (H) PCGF1-GFP pull outs with input (I, 1/90 th ), non-bound (NB, 1/90 th ), and bound (B, 1/3 rd ) and stained with antibodies directed against GFP, KDM2B, RING1B, USP7, and TRIM27. See also Figure S1 and , , and .

    Article Snippet: USP7 inhibitor P22077 , Merck , Cat# 662142.

    Techniques: Liquid Chromatography with Mass Spectroscopy, Methylation, Western Blot, Expressing, Mutagenesis, In Silico, Staining

    GFP-USP7 predominantly interacts with PRC1.1 (A) Confocal images of fixed K562 GFP-USP7 cells stained with DAPI. Scale bars represent 25 μm. (B) Western blots showing relative expression of GFP-USP7 versus endogenous USP7 in K562 cells and efficient precipitation of GFP-USP7 using GFP-Trap beads. Input (I, 1/90 th ), non-bound (NB, 1/90 th ), and bound (B, 1/3 rd ) are indicated. (C) Volcano plot showing enrichment of GFP-USP7-specific interaction partners in GFP and GFP-USP7 pull outs. Pull outs were performed in triplicate on K562 GFP and GFP-USP7 cells, and samples were analyzed using LC-MS/MS, followed by data analysis using MaxQuant and Perseus software. Statistical analysis was performed using Student's t test (false discovery rate (FDR) < 0.01; fold change (FC) > 10). PRC1.1, PRC1.2/1.4, and PRC1.6 subunits are indicated in red, blue, and purple respectively. (D) Volcano plot showing enrichment of previously identified USP7 interaction partners (orange), including the MRN-MDC1 complex (green). Statistical analysis was performed using Student's t test (false discovery rate (FDR) < 0.01; fold change (FC) > 10). (E) Intensity-based absolute quantification (iBAQ) value-based calculation of relative stoichiometry values relative to BCOR. (F) Western blot analysis of independent pull outs of GFP, PCGF1-GFP, PCGF2-GFP, PCGF4-GFP, GFP-RING1B, and GFP-CBX2 where input (I, 1/90 th ), non-bound (NB, 1/90 th ), and bound (B1/3 rd ) fractions are loaded and stained with USP7 and RING1B antibodies. See also .

    Journal: iScience

    Article Title: The USP7-TRIM27 axis mediates non-canonical PRC1.1 function and is a druggable target in leukemia

    doi: 10.1016/j.isci.2021.102435

    Figure Lengend Snippet: GFP-USP7 predominantly interacts with PRC1.1 (A) Confocal images of fixed K562 GFP-USP7 cells stained with DAPI. Scale bars represent 25 μm. (B) Western blots showing relative expression of GFP-USP7 versus endogenous USP7 in K562 cells and efficient precipitation of GFP-USP7 using GFP-Trap beads. Input (I, 1/90 th ), non-bound (NB, 1/90 th ), and bound (B, 1/3 rd ) are indicated. (C) Volcano plot showing enrichment of GFP-USP7-specific interaction partners in GFP and GFP-USP7 pull outs. Pull outs were performed in triplicate on K562 GFP and GFP-USP7 cells, and samples were analyzed using LC-MS/MS, followed by data analysis using MaxQuant and Perseus software. Statistical analysis was performed using Student's t test (false discovery rate (FDR) < 0.01; fold change (FC) > 10). PRC1.1, PRC1.2/1.4, and PRC1.6 subunits are indicated in red, blue, and purple respectively. (D) Volcano plot showing enrichment of previously identified USP7 interaction partners (orange), including the MRN-MDC1 complex (green). Statistical analysis was performed using Student's t test (false discovery rate (FDR) < 0.01; fold change (FC) > 10). (E) Intensity-based absolute quantification (iBAQ) value-based calculation of relative stoichiometry values relative to BCOR. (F) Western blot analysis of independent pull outs of GFP, PCGF1-GFP, PCGF2-GFP, PCGF4-GFP, GFP-RING1B, and GFP-CBX2 where input (I, 1/90 th ), non-bound (NB, 1/90 th ), and bound (B1/3 rd ) fractions are loaded and stained with USP7 and RING1B antibodies. See also .

    Article Snippet: USP7 inhibitor P22077 , Merck , Cat# 662142.

    Techniques: Staining, Western Blot, Expressing, Liquid Chromatography with Mass Spectroscopy, Software

    USP7 deubiquitinase activity is essential for PRC1.1 integrity (A) Purification of His-tagged ubiquitinated proteins under denaturing conditions in GFP-RING1B and PCGF1-GFP cells treated with DMSO or P22077 for 24 h (30 μM) followed by western blot analysis. (B) Volcano plot showing differential interaction of GFP-RING1B (left) and PCGF1-GFP (right; both indicated in green) with PRC1.1 subunits (highlighted in orange) as measured by label-free quantification (LFQ) of LC-MS/MS data in triplicate. The UBB protein is indicated in blue. Statistical analysis was performed using Student's t test (false discovery rate (FDR) < 0.1; fold change (FC) > 2). (C) Intensity-based absolute quantification (iBAQ) value ratios of several identified PRC1.1 proteins as identified in GFP-RING1B (left) and PCGF1-GFP (right) pull outs from P22077- or DMSO-treated cells. Data are shown as mean ± SD (n = 2 or 3). (D) Western blot of GFP pull outs on PCGF1-GFP and GFP-RING1B in the absence (−) or presence (+) of P22077 (72 h, 30 μM) probed with antibodies for GFP, RING1B, and PCGF1. Input (I, 1/90 th ), non-bound (NB, 1/90 th ), and bound (B, 1/3 rd ) fractions are shown. (E) Mean fluorescent intensity (MFI) analysis of K562 cells expressing either GFP-RING1B, PCGF1-GFP, or KDM2B-GFP treated with DMSO or P22077 for 72 h. See also .

    Journal: iScience

    Article Title: The USP7-TRIM27 axis mediates non-canonical PRC1.1 function and is a druggable target in leukemia

    doi: 10.1016/j.isci.2021.102435

    Figure Lengend Snippet: USP7 deubiquitinase activity is essential for PRC1.1 integrity (A) Purification of His-tagged ubiquitinated proteins under denaturing conditions in GFP-RING1B and PCGF1-GFP cells treated with DMSO or P22077 for 24 h (30 μM) followed by western blot analysis. (B) Volcano plot showing differential interaction of GFP-RING1B (left) and PCGF1-GFP (right; both indicated in green) with PRC1.1 subunits (highlighted in orange) as measured by label-free quantification (LFQ) of LC-MS/MS data in triplicate. The UBB protein is indicated in blue. Statistical analysis was performed using Student's t test (false discovery rate (FDR) < 0.1; fold change (FC) > 2). (C) Intensity-based absolute quantification (iBAQ) value ratios of several identified PRC1.1 proteins as identified in GFP-RING1B (left) and PCGF1-GFP (right) pull outs from P22077- or DMSO-treated cells. Data are shown as mean ± SD (n = 2 or 3). (D) Western blot of GFP pull outs on PCGF1-GFP and GFP-RING1B in the absence (−) or presence (+) of P22077 (72 h, 30 μM) probed with antibodies for GFP, RING1B, and PCGF1. Input (I, 1/90 th ), non-bound (NB, 1/90 th ), and bound (B, 1/3 rd ) fractions are shown. (E) Mean fluorescent intensity (MFI) analysis of K562 cells expressing either GFP-RING1B, PCGF1-GFP, or KDM2B-GFP treated with DMSO or P22077 for 72 h. See also .

    Article Snippet: USP7 inhibitor P22077 , Merck , Cat# 662142.

    Techniques: Activity Assay, Purification, Western Blot, Liquid Chromatography with Mass Spectroscopy, Expressing

    USP7 inhibition induces loss of PRC1.1 occupancy and H2AK119ub at target loci (A) ChIP-qPCRs on K562, K562 GFP-RING1B, and K562 PCGF1-GFP cells, treated with DMSO or P22077 (72 h, 30 μM), using antibodies against KDM2B or GFP. (B and C) ChIP-qPCRs on K562 cells using antibodies directed against H2AK119ub (B), H3K4me3 (C), on several PRC1.1 loci. Error bars represent SD of technical qPCR replicates. (D and E) ChIP-qPCRs on DMSO- or P22077-treated K562 cells for 4 h, 8 h, and 16 h using antibodies against H2AK119ub (D), GFP (reading out KDM2B-GFP and GFP-RING1B), and H3K27ac (E) on various PRC1.1 loci. Error bars represent SD of technical qPCR replicates. (F) ChIP-qPCRs on K562 cells treated with either DMSO or FT671 (48 h, 10 μM) using antibodies against KDM2B and H2AK119ub. Error bars represent SD of three biological replicate experiments. See also <xref ref-type=Figure S2 . " width="100%" height="100%">

    Journal: iScience

    Article Title: The USP7-TRIM27 axis mediates non-canonical PRC1.1 function and is a druggable target in leukemia

    doi: 10.1016/j.isci.2021.102435

    Figure Lengend Snippet: USP7 inhibition induces loss of PRC1.1 occupancy and H2AK119ub at target loci (A) ChIP-qPCRs on K562, K562 GFP-RING1B, and K562 PCGF1-GFP cells, treated with DMSO or P22077 (72 h, 30 μM), using antibodies against KDM2B or GFP. (B and C) ChIP-qPCRs on K562 cells using antibodies directed against H2AK119ub (B), H3K4me3 (C), on several PRC1.1 loci. Error bars represent SD of technical qPCR replicates. (D and E) ChIP-qPCRs on DMSO- or P22077-treated K562 cells for 4 h, 8 h, and 16 h using antibodies against H2AK119ub (D), GFP (reading out KDM2B-GFP and GFP-RING1B), and H3K27ac (E) on various PRC1.1 loci. Error bars represent SD of technical qPCR replicates. (F) ChIP-qPCRs on K562 cells treated with either DMSO or FT671 (48 h, 10 μM) using antibodies against KDM2B and H2AK119ub. Error bars represent SD of three biological replicate experiments. See also Figure S2 .

    Article Snippet: USP7 inhibitor P22077 , Merck , Cat# 662142.

    Techniques: Inhibition

    Genome-wide loss of H2AK119ub upon USP7 inhibition (A–D) ChIP-seq on K562 cells treated with either DMSO or FT671 (24 h, 10 μM) using antibodies against H2AK119ub, H3K4me3, H3K36me3, or H3K27me3. (A) Venn diagram depicting overlapping peaks −/+ 5kb from the transcription start site (TSS). (B) Density plots displaying epimarks around the TSS or across the gene body until + 5kb after the transcription end site (TES). (C) Heat maps of the H2AK119ub signal around the TSS. (D) Representative screenshots of epimarks at four PRC1.1 loci. (E) Non-canonical PRC1.1 or canonical PRC1 peaks shared between six primary AML CD34 + patient samples ( <xref ref-type=van den Boom et al., 2016 ) were overlaid with USP7 peaks from CUTTL1 cells ( Jin et al., 2019 ). (F) Representative screens shots of PRC1.1 and PRC1 loci depicting USP7 and KDM2B binding and H3K27me3 levels. See also Figure S3 . " width="100%" height="100%">

    Journal: iScience

    Article Title: The USP7-TRIM27 axis mediates non-canonical PRC1.1 function and is a druggable target in leukemia

    doi: 10.1016/j.isci.2021.102435

    Figure Lengend Snippet: Genome-wide loss of H2AK119ub upon USP7 inhibition (A–D) ChIP-seq on K562 cells treated with either DMSO or FT671 (24 h, 10 μM) using antibodies against H2AK119ub, H3K4me3, H3K36me3, or H3K27me3. (A) Venn diagram depicting overlapping peaks −/+ 5kb from the transcription start site (TSS). (B) Density plots displaying epimarks around the TSS or across the gene body until + 5kb after the transcription end site (TES). (C) Heat maps of the H2AK119ub signal around the TSS. (D) Representative screenshots of epimarks at four PRC1.1 loci. (E) Non-canonical PRC1.1 or canonical PRC1 peaks shared between six primary AML CD34 + patient samples ( van den Boom et al., 2016 ) were overlaid with USP7 peaks from CUTTL1 cells ( Jin et al., 2019 ). (F) Representative screens shots of PRC1.1 and PRC1 loci depicting USP7 and KDM2B binding and H3K27me3 levels. See also Figure S3 .

    Article Snippet: USP7 inhibitor P22077 , Merck , Cat# 662142.

    Techniques: Genome Wide, Inhibition, ChIP-sequencing, Binding Assay

    Loss of TRIM27 partially rescues USP7 inhibitor sensitivity (A) Knockdown efficiencies of two independent TRIM27 shRNAs in K562 cells. Error bars represent SD from technical triplicates. (B) KDM2B-GFP and H2AK119ub ChIP-qPCRs with error bars representing SD based on three independent experiments, statistical analysis was performed using Student's t test; ∗p < 0.05 and ∗∗p < 0.01. (C) Western blot analysis of KDM2B-GFP pull outs on K562 cells expressing SCR or TRIM27 (#1) shRNAs using the indicated antibodies. Input (I, 1/90 th ), non-bound (NB, 1/90 th ), and bound (B, 1/3 rd ) as indicated. (D) H2AK119ub ChIP-qPCR on K562 cells expressing SCR or TRIM27 (#2) shRNAs and treated with DMSO or FT671 (48 h, 10μM). Error bars represent SD based on three independent experiments; statistical analysis was performed using Student's t test; ∗p < 0.05 and ∗∗p < 0.01. (E) Cumulative cell proliferation of K562 cells expressing SCR or TRIM27 (#1 or #2) shRNAs and treated with DMSO or FT671. Error bars represent SD based on two independent experiments. (F) Knockdown efficiencies of two independent USP7 shRNAs in K562 cells. Error bars represent SD from technical triplicates. (G) Western blot analysis of KDM2B-GFP pull outs on K562 cells expressing SCR or USP7 (#1 and #2) shRNAs using the indicated antibodies. Input (I, 1/90 th ), non-bound (NB, 1/90 th ), and bound (B, 1/3 rd ) as indicated. (H) Endogenous KDM2B and H2AK119ub ChIP-qPCRs on K562 cells expressing SCR of USP7 (#1 and #2) shRNAs. Error bars represent SD based on three independent experiments; statistical analysis was performed using Student's t test; ∗p < 0.05 and ∗∗p < 0.01. (I) Western blot analysis of THP-1 doxycycline-inducible CRISPR/Cas9 USP7 knockout cells treated with doxycycline for 3 days and subsequent culture for 4 days and stained with the indicated antibodies. (J) Endogenous KDM2B and H2AK119ub ChIP-qPCRs on doxycycline-treated cells (day 6). Error bars represent SD based on three independent experiments; statistical analysis was performed using Student's t test; ∗p < 0.05 and ∗∗p < 0.01. (K) Graphical abstract of effects of USP7 inhibition versus USP7 or TRIM27 knockdown. See also <xref ref-type=Figure S4 . " width="100%" height="100%">

    Journal: iScience

    Article Title: The USP7-TRIM27 axis mediates non-canonical PRC1.1 function and is a druggable target in leukemia

    doi: 10.1016/j.isci.2021.102435

    Figure Lengend Snippet: Loss of TRIM27 partially rescues USP7 inhibitor sensitivity (A) Knockdown efficiencies of two independent TRIM27 shRNAs in K562 cells. Error bars represent SD from technical triplicates. (B) KDM2B-GFP and H2AK119ub ChIP-qPCRs with error bars representing SD based on three independent experiments, statistical analysis was performed using Student's t test; ∗p < 0.05 and ∗∗p < 0.01. (C) Western blot analysis of KDM2B-GFP pull outs on K562 cells expressing SCR or TRIM27 (#1) shRNAs using the indicated antibodies. Input (I, 1/90 th ), non-bound (NB, 1/90 th ), and bound (B, 1/3 rd ) as indicated. (D) H2AK119ub ChIP-qPCR on K562 cells expressing SCR or TRIM27 (#2) shRNAs and treated with DMSO or FT671 (48 h, 10μM). Error bars represent SD based on three independent experiments; statistical analysis was performed using Student's t test; ∗p < 0.05 and ∗∗p < 0.01. (E) Cumulative cell proliferation of K562 cells expressing SCR or TRIM27 (#1 or #2) shRNAs and treated with DMSO or FT671. Error bars represent SD based on two independent experiments. (F) Knockdown efficiencies of two independent USP7 shRNAs in K562 cells. Error bars represent SD from technical triplicates. (G) Western blot analysis of KDM2B-GFP pull outs on K562 cells expressing SCR or USP7 (#1 and #2) shRNAs using the indicated antibodies. Input (I, 1/90 th ), non-bound (NB, 1/90 th ), and bound (B, 1/3 rd ) as indicated. (H) Endogenous KDM2B and H2AK119ub ChIP-qPCRs on K562 cells expressing SCR of USP7 (#1 and #2) shRNAs. Error bars represent SD based on three independent experiments; statistical analysis was performed using Student's t test; ∗p < 0.05 and ∗∗p < 0.01. (I) Western blot analysis of THP-1 doxycycline-inducible CRISPR/Cas9 USP7 knockout cells treated with doxycycline for 3 days and subsequent culture for 4 days and stained with the indicated antibodies. (J) Endogenous KDM2B and H2AK119ub ChIP-qPCRs on doxycycline-treated cells (day 6). Error bars represent SD based on three independent experiments; statistical analysis was performed using Student's t test; ∗p < 0.05 and ∗∗p < 0.01. (K) Graphical abstract of effects of USP7 inhibition versus USP7 or TRIM27 knockdown. See also Figure S4 .

    Article Snippet: USP7 inhibitor P22077 , Merck , Cat# 662142.

    Techniques: Western Blot, Expressing, CRISPR, Knock-Out, Staining, Inhibition

    USP7 inhibition leads to transcriptional changes of PRC1.1 target genes (A) Unsupervised clustering of RNA-seq data from three independent experiments where K562 cells were treated with DMSO or FT671 (10μM, 48 h) samples. (B) Venn diagram showing overlap of significantly up- and downregulated genes (Student's t test, p < 1x10 −6 ) with previously identified PRC1.1 target genes. (C) GSEA analysis showing enrichment score against ranked RNA-seq data. RNA-seq data were compared with indicated gene sets. (D) Gene ontology analyses of regulatory processes (RP) of all up- and downregulated genes in FT671-treated cells. (E) Gene ontology analyses of regulatory processes (RP) of up- and downregulated genes in FT671-treated cells that are also targeted by PRC1.1. (F) Screens shots of our ChIP-seq tracks ( <xref ref-type=van den Boom et al., 2016 ) for H2AK119ub, H3K27me3, PCGF1, PCGF2, PCGF4, CBX2, RING1A, RING1B, and KDM2B (all GFP-fusions) in K562 cells. ChIP-seq tracks for H3K4me3, H3K36me3, RNAPII, H3K27ac, EZH2, SUZ12 (all K562), and USP7 (CUTLL1) were downloaded from ENCODE/Broad. In addition, endogenous KDM2B, H2AK119ub, H3K27me3, and H3K4me3 in two primary AML patient cell samples are shown. See also Figure S5 . " width="100%" height="100%">

    Journal: iScience

    Article Title: The USP7-TRIM27 axis mediates non-canonical PRC1.1 function and is a druggable target in leukemia

    doi: 10.1016/j.isci.2021.102435

    Figure Lengend Snippet: USP7 inhibition leads to transcriptional changes of PRC1.1 target genes (A) Unsupervised clustering of RNA-seq data from three independent experiments where K562 cells were treated with DMSO or FT671 (10μM, 48 h) samples. (B) Venn diagram showing overlap of significantly up- and downregulated genes (Student's t test, p < 1x10 −6 ) with previously identified PRC1.1 target genes. (C) GSEA analysis showing enrichment score against ranked RNA-seq data. RNA-seq data were compared with indicated gene sets. (D) Gene ontology analyses of regulatory processes (RP) of all up- and downregulated genes in FT671-treated cells. (E) Gene ontology analyses of regulatory processes (RP) of up- and downregulated genes in FT671-treated cells that are also targeted by PRC1.1. (F) Screens shots of our ChIP-seq tracks ( van den Boom et al., 2016 ) for H2AK119ub, H3K27me3, PCGF1, PCGF2, PCGF4, CBX2, RING1A, RING1B, and KDM2B (all GFP-fusions) in K562 cells. ChIP-seq tracks for H3K4me3, H3K36me3, RNAPII, H3K27ac, EZH2, SUZ12 (all K562), and USP7 (CUTLL1) were downloaded from ENCODE/Broad. In addition, endogenous KDM2B, H2AK119ub, H3K27me3, and H3K4me3 in two primary AML patient cell samples are shown. See also Figure S5 .

    Article Snippet: USP7 inhibitor P22077 , Merck , Cat# 662142.

    Techniques: Inhibition, RNA Sequencing Assay, ChIP-sequencing

    Sensitivity of AML cells toward USP7 inhibition (A) Cumulative cell growth of various AML cell lines treated with DMSO or various concentrations of P22077. (B) Cumulative cell growth of various AML cell lines treated with DMSO or various concentrations of FT671. Error bars represent SD based on measurement of biological triplicates. (C) Cumulative cell growth of primary AML patient cells (n = 3) grown on MS5 stromal cells treated with DMSO (control) or P22077. Error bars represent SD based on measurement of biological duplicates. (D) Cumulative cell growth of primary AML patient cells (n = 3) grown on MS5 stromal cells treated with DMSO or FT671. Error bars represent SD based on measurement of biological duplicates. (E) Viable cell numbers after 8 days of treatment with DMSO or increasing concentrations of FT671. Representative examples of primary AML patient cells and cord blood CD34 + cell samples are shown. Error bars represent SD based on measurement of biological triplicates. (F) IC50 curves and data for 11 independent primary AML samples, cord blood CD34 + cells, and mobilized peripheral blood stem cells (PBSCs), cocultured on MS5 stromal cells for 8 days in the presence of increasing amounts of FT671. Asterisk indicates TP53-mutant AMLs. (G) Experimental setup of our human CB MLL-AF9 xenograft mouse model. Here 5 x 10 4 MLL-AF9 GFP + cells from a primary leukemic mouse were IV injected into secondary recipients (n = 11). (H) Peripheral blood analysis of MLL-AF9 GFP/CD45 + cells, three weeks after injection prior to treatment (left) and 2.5 weeks following treatment (right). Mice were treated daily with either DMSO as control (n = 5) or 20 mg/kg P22077 (n = 6). (I) Peripheral blood chimerism levels of control and P22077 (20 mg/kg)-treated mice over the course of the experiment. Treatment was started at day 28 (4 weeks post-transplant) as indicated with an arrow. See also <xref ref-type=Figure S6 . " width="100%" height="100%">

    Journal: iScience

    Article Title: The USP7-TRIM27 axis mediates non-canonical PRC1.1 function and is a druggable target in leukemia

    doi: 10.1016/j.isci.2021.102435

    Figure Lengend Snippet: Sensitivity of AML cells toward USP7 inhibition (A) Cumulative cell growth of various AML cell lines treated with DMSO or various concentrations of P22077. (B) Cumulative cell growth of various AML cell lines treated with DMSO or various concentrations of FT671. Error bars represent SD based on measurement of biological triplicates. (C) Cumulative cell growth of primary AML patient cells (n = 3) grown on MS5 stromal cells treated with DMSO (control) or P22077. Error bars represent SD based on measurement of biological duplicates. (D) Cumulative cell growth of primary AML patient cells (n = 3) grown on MS5 stromal cells treated with DMSO or FT671. Error bars represent SD based on measurement of biological duplicates. (E) Viable cell numbers after 8 days of treatment with DMSO or increasing concentrations of FT671. Representative examples of primary AML patient cells and cord blood CD34 + cell samples are shown. Error bars represent SD based on measurement of biological triplicates. (F) IC50 curves and data for 11 independent primary AML samples, cord blood CD34 + cells, and mobilized peripheral blood stem cells (PBSCs), cocultured on MS5 stromal cells for 8 days in the presence of increasing amounts of FT671. Asterisk indicates TP53-mutant AMLs. (G) Experimental setup of our human CB MLL-AF9 xenograft mouse model. Here 5 x 10 4 MLL-AF9 GFP + cells from a primary leukemic mouse were IV injected into secondary recipients (n = 11). (H) Peripheral blood analysis of MLL-AF9 GFP/CD45 + cells, three weeks after injection prior to treatment (left) and 2.5 weeks following treatment (right). Mice were treated daily with either DMSO as control (n = 5) or 20 mg/kg P22077 (n = 6). (I) Peripheral blood chimerism levels of control and P22077 (20 mg/kg)-treated mice over the course of the experiment. Treatment was started at day 28 (4 weeks post-transplant) as indicated with an arrow. See also Figure S6 .

    Article Snippet: USP7 inhibitor P22077 , Merck , Cat# 662142.

    Techniques: Inhibition, Mutagenesis, Injection

    Journal: iScience

    Article Title: The USP7-TRIM27 axis mediates non-canonical PRC1.1 function and is a druggable target in leukemia

    doi: 10.1016/j.isci.2021.102435

    Figure Lengend Snippet:

    Article Snippet: USP7 inhibitor P22077 , Merck , Cat# 662142.

    Techniques: Recombinant, Blocking Assay, Plasmid Preparation, Software, Purification, SYBR Green Assay