Journal: The Journal of Biological Chemistry

Article Title: Upregulation of CYR61 by TGF-β and YAP signaling exerts a counter-suppression of hepatocellular carcinoma

doi: 10.1016/j.jbc.2024.107208

Figure Lengend Snippet: TGF-β and Hippo signaling coordinately regulate CYR61 gene transcription. A and B , HCCLM3 or HLE cells were treated with 2.5 ng/ml of TGF-β1 in the presence or absence of small chemical inhibitors of different signaling pathways for 24 h, followed by gene expression analyses by quantitative PCR ( A ) or Western blotting ( B ). TGF-β type I receptor inhibitor, SB431542 (5 μM); YAP inhibitor, verteporfin (5 μM); MEK inhibitor, PD0325901 (5 μM); JNK inhibitor, SP600125 (5 μM); GSK-3 inhibitor, SB216763 (5 μM); NF-κB inhibitor, JSH-23 (5 μM); PI3K inhibitor, LY294002 (5 μM); ERK1/2 inhibitor, LY3214996 (5 μM). C , HLE or HCCLM3 cells treated with 2.5 ng/ml of TGF-β1 and/or 3 μM of XMU-MP-1 for 24 h were harvested for protein expression detection by Western blotting. D and E , HLE or HCCLM3 cells were treated with 2.5 ng/ml of TGF-β1 ( D ) or 3 μM of XMU-MP-1 ( E ) for 24 h, in the presence or absence of 5 μM of SB431542 and/or 5 μM of verteporfin. Then cells were analyzed by Western blotting. F and G , liver cancer cells transfected with siRNAs were treated with or without 2.5 ng/ml of TGF-β1 ( F ) or 3 μM of XMU-MP-1 ( G ) for 24 h before being harvested for Western blotting analyses. TGF-β, transforming growth factor-β.

Article Snippet: Small chemical inhibitors, such as JSH-23 (HY-13982), SB216763 (HY-12012), verteporfin (HY-B0146), SB431542 (HY-10431), PD0325901 (HY-131295), SP600125 (HY-12041), LY3214996 (HY-101494), and LY294002 (HY-10108), were all purchased from MedChemExpress (MCE), while XMU-MP-1 was obtained from AbMole (M9057).

Techniques: Protein-Protein interactions, Gene Expression, Real-time Polymerase Chain Reaction, Western Blot, Expressing, Transfection

Journal: iScience

Article Title: Electrically synchronizing and modulating the dynamics of ERK activation to regulate cell fate

doi: 10.1016/j.isci.2021.103240

Figure Lengend Snippet:

Article Snippet: PD325901 MEK inhibitor , Cell signaling , Cat#79241S.

Techniques: Recombinant, Plasmid Preparation, Software

Journal: Nature Communications

Article Title: Identifying regulators of parental imprinting by CRISPR/Cas9 screening in haploid human embryonic stem cells

doi: 10.1038/s41467-021-26949-7

Figure Lengend Snippet: a Schematic overview of the loss-of-function screen experimental setup. Haploid parthenogenetic hESCs infected with a genome-wide CRISPR/Cas9 sgRNA library, were stained with an antibody against the paternally expressed gene PEG10 (normally silenced in these cells). This was followed by FACS sorting to isolate the PEG10-positive (PEG10 + ) cell population. Finally, targeted DNA sequencing of sgRNAs identifies enriched genes mutated in PEG10 + cells compared with unsorted control. b Histogram showing the flow cytometry analysis of PEG10 staining in androgenetic (blue) vs. parthenogenetic (red) cells. c Representative scatter plots of the flow cytometry analysis of PEG10 staining in secondary only control (left), haploid parthenogenetic CRISPR/Cas9 library cells (center) and bi-parental cells (right). y Axis represents the fluorescence intensity of PEG10 staining, while the x axis represents the autofluorescence signal. d Volcano plot showing the median log 2 fold change (FC) of normalized sgRNA read counts (calculated by edgeR) per gene, between PEG10 + and unsorted control ( x axis, values are normalized to zero. n = 4 replicate screens). y Axis represents −log 10 of the P value (two-sample, two-sided Kolmogorov-Smirnov test). Marked in blue are enriched genes having log FC > 0.5 (equivalent to normalized value >1.4) and P value < 0.05. Representative genes included in the “EpiFactors” database (orange), zinc finger proteins (purple) and tumor suppressors (blue) are indicated. e Pie chart subgrouping the 115 candidate genes by function (after removing genes enriched in the PEG10-negative control). Chromatin-related genes are further divided to subcategories: Genes included in the EpiFactors database, genes encoding zinc finger proteins (ZNFP) and those encoding transcription factors (TF). f Mean expression FC of PEGs between hpESCs treated with the MEK/ERK inhibitor PD0325901 and DMSO. n = 4 replicates from each treatment in two different cell lines. Data are presented as mean ± SEM. Shown are PEGs with FC > 1. P values are listed in gray (one-tailed, paired t -test).

Article Snippet: Then bFGF (FGF2) was removed from the medium with addition of 25 μM PD0325901 (Biogems #3911091) or 0.1% DMSO as control for 5 days.

Techniques: Infection, Genome Wide, CRISPR, Staining, DNA Sequencing, Control, Flow Cytometry, Fluorescence, Negative Control, Expressing, One-tailed Test

Journal: Molecular cell

Article Title: Members of an array of zinc finger proteins specify distinct Hox chromatin boundaries

doi: 10.1016/j.molcel.2024.08.007

Figure Lengend Snippet: Key Resources Table

Article Snippet: MEK1/2 inhibitor (PD0325901) , Stemgent , #04-0006-base.

Techniques: Virus, Recombinant, Magnetic Beads, SYBR Green Assay, Western Blot, Clone Assay, Plasmid Preparation, Software, Injection