Journal: Cell Death & Disease

Article Title: Identification of targetable epigenetic vulnerabilities for uveal melanoma

doi: 10.1038/s41419-025-08295-4

Figure Lengend Snippet: A Mean viability of the three UM cell lines following 72 h treatment with 932 epigenetic modulators at a concentration of 1 μM ( n = 2) relative to the negative control (0.1% DMSO treatment). Hit cut-offs (dashed lines) were determined as the mean percentage viability of the negative controls in each cell line minus three standard deviations. Yellow dashed line is the hit cut-off for MP41 cells (65.8% viability), purple dashed line is the hit cut-off for MP46 cells (74.0% viability), and the green dashed line is the hit cut-off for MP38 cells (58.9% viability). For full list of compounds and average UM cell viabilities, see Supplementary Data . B Radar plot showing the mean difference in percent of cell viability of UM cells caused by 72 h 1 μM treatment with 932 compounds, relative to the DMSO control. Negative values, shown in gray, indicate ineffective compounds leading to greater cell viability than the negative control. The positive values, shown in color, indicate compounds that induced cell death, with higher peaks indicating greater cell death. Compounds are grouped by drug mechanism of action. C Pie charts of the molecular activities of all screened compounds ( n = 932) (left) and the hits identified ( n = 24) (right). D Concentration-response experiments for the 24 hit compounds (10 concentrations, n = 4 per concentration per cell line). Center values represent mean viability, error bars represent standard error of mean (SEM). E Log IC 50 (M) values of the top hit compounds for each cell line. Error bars represent 95% confidence interval. F Log IC 50 (M) of BAP1 mutant cell lines (MP46 and MP38) plotted against the log IC 50 (M) of the BAP1 wildtype cell line (MP41) for each drug treatment.

Article Snippet: Given the global epigenetic changes elicited by BAP1 loss, we performed a comprehensive epigenetic compound screen on UM cells, using a well-characterized drug library consisting of 932 cell-permeable, small-molecule modulators (TargetMol, L1200, July 2022; Supplementary Data ).

Techniques: Concentration Assay, Negative Control, Control, Mutagenesis

Journal: Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie

Article Title: Tandem mass tag (TMT) proteomic analysis of fetal lungs revealed differential expression of tight junction proteins in a rat model of congenital diaphragmatic hernia.

doi: 10.1016/j.biopha.2019.109621

Figure Lengend Snippet: Fig. 6. Western blotting analysis of tight junction protein expression in the lungs of fetal rats. (A, B) Representative immunoblotting and densitometric analysis of tight junction protein expression in the fetal lung. Results were normalized relative to the expres- sion of β-actin (n = 6 per group, *P < 0.05, vs. con- trol). Western blot analysis showed increased levels of Cldn3 and decreased levels of Magi1 and Myh9 in the CDH fetal lungs.

Article Snippet: The membranes were blocked in 5% nonfat dry milk for 60min and then incubated with rabbit polyclonal anti-CLDN3 (Proteintech, Chicago, USA), rabbit polyclonal anti-MAGI1 antibody (Absin, Shanghai, China), rabbit polyclonal anti-MYH9 (Proteintech Group, Chicago, USA), and mouse monoclonal β-actin (Proteintech Group, Chicago, USA) overnight at 4 °C.

Techniques: Western Blot, Expressing

Journal: Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie

Article Title: Tandem mass tag (TMT) proteomic analysis of fetal lungs revealed differential expression of tight junction proteins in a rat model of congenital diaphragmatic hernia.

doi: 10.1016/j.biopha.2019.109621

Figure Lengend Snippet: Fig. 7. IHC analysis of tight-junction proteins in the lungs of fetal rats. (A) Representative photomicrographs of IHC-staining for Cldn3, Magi1, and Myh9 in the lung sections from CDH (Left panel) and Control (right panel) fetal rats. (Original magnification ×400, scale bar = 100 μm). Cldn3 and Magi1 were mainly expressed in the epithelial cells, and some weak staining was also found in the mesenchymal cells. Myh9 protein localized to both epithelial and mesenchymal cells. (B) Semi‑quantitative analysis of IHC staining (mean density). n = 3 per group, *P < 0.05, vs. control.

Article Snippet: The membranes were blocked in 5% nonfat dry milk for 60min and then incubated with rabbit polyclonal anti-CLDN3 (Proteintech, Chicago, USA), rabbit polyclonal anti-MAGI1 antibody (Absin, Shanghai, China), rabbit polyclonal anti-MYH9 (Proteintech Group, Chicago, USA), and mouse monoclonal β-actin (Proteintech Group, Chicago, USA) overnight at 4 °C.

Techniques: Immunohistochemistry, Control, Staining

Journal: Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie

Article Title: Tandem mass tag (TMT) proteomic analysis of fetal lungs revealed differential expression of tight junction proteins in a rat model of congenital diaphragmatic hernia.

doi: 10.1016/j.biopha.2019.109621

Figure Lengend Snippet: Fig. 8. Temporal expression of tight junction mRNA in CDH lungs. (A–C) Cldn3, Magi1, and Myh9 mRNA levels in CDH lungs were determined by quantitative RT- PCR at different time points. β-actin was used as a housekeeping gene. The results were normalized relative to the same-aged control group (n = 8 per group, *P < 0.05, vs. control at the same time point).

Article Snippet: The membranes were blocked in 5% nonfat dry milk for 60min and then incubated with rabbit polyclonal anti-CLDN3 (Proteintech, Chicago, USA), rabbit polyclonal anti-MAGI1 antibody (Absin, Shanghai, China), rabbit polyclonal anti-MYH9 (Proteintech Group, Chicago, USA), and mouse monoclonal β-actin (Proteintech Group, Chicago, USA) overnight at 4 °C.

Techniques: Expressing, Quantitative RT-PCR, Control

Journal: BMB Reports

Article Title: BAP1 controls mesenchymal stem cell migration by inhibiting the ERK signaling pathway

doi: 10.5483/BMBRep.2023-0174

Figure Lengend Snippet: BAP1 depletion promotes MSC migration. (A) A table of the siRNA screening results. (B-G) The MSCs were transfected with 20 nM siNon or deubiquitinase siRNAs. The cells were scratched, visualized by a bright field microscope (E), and further analyzed using Image the J software (B, C). Data are presented as the mean ± standard deviation (SD) from three independent experiments. Statistical analysis was performed using two-way ANOVA. Significances were computed by Tukey’s honestly significant difference (HSD) (*P < 0.05, **P < 0.01, and ***P < 0.001). (D) BAP1 protein levels were determined by immunoblotting. For the transwell migration (F) and invasion analysis (G), data are presented as the mean ± SD from three independent experiments. Statistical analysis was performed using Student’s t-test (**P < 0.01 and ***P < 0.001).

Article Snippet: Furthermore, the BAP1 expression pattern observed in the Human Protein Atlas supports an inverse correlation between BAP1 expression and cell motility, with blood cells, known for their high motility, showing notably lower levels of BAP1 expression ( of the SI).

Techniques: Migration, Transfection, Microscopy, Software, Standard Deviation, Western Blot

Journal: BMB Reports

Article Title: BAP1 controls mesenchymal stem cell migration by inhibiting the ERK signaling pathway

doi: 10.5483/BMBRep.2023-0174

Figure Lengend Snippet: BAP1 expression hinders MSC migration. (A) MSCs, 24 h post-pCGfd-GFP transfection, were visualized using a fluorescence microscope. (B) MSCs transfected with pCGfd-GFP or -HA-BAP1 were harvested for immunoblot analysis. (C, D) Cells were scratched, visualized by a bright field microscope, and further analyzed using the Image J software. Data are presented as the mean ± SD from three independent experiments. Statistical analysis was performed using two-way ANOVA. Significance was calculated using Tukey’s HSD (***P < 0.001). (E, F) Transwell migration or invasion assays were performed. Data are presented as the mean ± SD from three independent experiments. Statistical analysis was performed using a Student’s t-test (*P < 0.05 and **P < 0.01).

Article Snippet: Furthermore, the BAP1 expression pattern observed in the Human Protein Atlas supports an inverse correlation between BAP1 expression and cell motility, with blood cells, known for their high motility, showing notably lower levels of BAP1 expression ( of the SI).

Techniques: Expressing, Migration, Transfection, Fluorescence, Microscopy, Western Blot, Software

Journal: BMB Reports

Article Title: BAP1 controls mesenchymal stem cell migration by inhibiting the ERK signaling pathway

doi: 10.5483/BMBRep.2023-0174

Figure Lengend Snippet: BAP1 suppresses the ERK signaling pathway. (A, B) MSCs transfected with 20 nM siNon or siBAP1 were harvested for immunoblot analysis. (C) The levels of mRNA were determined using qRT-PCR. Data are presented as the mean ± SD from three independent experiments. Statistical analysis was performed using Student’s t-test (ns = non-significant, *P < 0.05 and **P < 0.01).

Article Snippet: Furthermore, the BAP1 expression pattern observed in the Human Protein Atlas supports an inverse correlation between BAP1 expression and cell motility, with blood cells, known for their high motility, showing notably lower levels of BAP1 expression ( of the SI).

Techniques: Transfection, Western Blot, Quantitative RT-PCR

Journal: BMB Reports

Article Title: BAP1 controls mesenchymal stem cell migration by inhibiting the ERK signaling pathway

doi: 10.5483/BMBRep.2023-0174

Figure Lengend Snippet: BAP1 binds to ERK1/2 and regulates its ubiquitination status in a deubiquitinase activity-dependent manner. (A, C, E) 293T cells transfected with the indicated plasmids were harvested, lysed, and immunoprecipitated with an anti-GFP antibody. Thereafter, proteins were analyzed by immunoblotting using anti-FLAG and -GFP antibodies. (B) MSCs were lysed and immunoprecipitated using an anti-BAP1 antibody. Endogenous proteins were analyzed by immunoblotting using the indicated antibodies. (D, F) 293T cells transfected with the indicated plasmids were harvested, lysed under denaturing conditions, and immunoprecipitated with an anti-GFP antibody. Protein levels were analyzed by immunoblotting using anti-ubiquitin-HRP, -GFP, and -FLAG antibodies. (G) MSCs transfected with 20 nM siNon or siBAP1 were lysed under denaturing conditions and immunoprecipitated with an anti-ERK1/2 antibody. Proteins were analyzed by immunoblotting using the indicated antibodies. (H) Conceptual illustration showing the role of BAP1 in regulating MSC migration.

Article Snippet: Furthermore, the BAP1 expression pattern observed in the Human Protein Atlas supports an inverse correlation between BAP1 expression and cell motility, with blood cells, known for their high motility, showing notably lower levels of BAP1 expression ( of the SI).

Techniques: Ubiquitin Proteomics, Activity Assay, Transfection, Immunoprecipitation, Western Blot, Migration