Journal: Stem cell reports

Article Title: DOT1L regulates lung developmental epithelial cell fate and adult alveolar stem cell differentiation after acute injury.

doi: 10.1016/j.stemcr.2023.07.006

Figure Lengend Snippet: Figure 1. Alveolar organoid screen to identify epigenetic pathways regulating alveolar regeneration (A) Schematic of how AT2 cells isolated from SftpcEGFP mice were used in the screen. (B) An example of fluorescent reporter detection from SftpcEGFP AT2 cells in a 96-well plate. Arrows indicate negative (water or DMSO) or positive (FGF7) controls used for the screen. (C) Results from the epigenetic small molecular inhibitor library using a Z score of 2.0 as a cutoff for a positive increase in alveolar organoid total fluorescence. Data are representative of the screening assay performed in duplicate.

Article Snippet: Forty-eight hours after seeding cells, medium was changed to include 10 mM of one small molecule from the epigenetic library (Selleckchem, L1900) or an equal volume of H2O or DMSO as negative controls and 50 ng/mL of Fgf7 as a positive control.

Techniques: Isolation, Screening Assay

Journal: Stem cell reports

Article Title: DOT1L regulates lung developmental epithelial cell fate and adult alveolar stem cell differentiation after acute injury.

doi: 10.1016/j.stemcr.2023.07.006

Figure Lengend Snippet: Figure 7. Model of how Dot1l regulation of AT2-AT1 differentiation through regula- tion of OxPhos and a subset of transcrip- tion and epigenetic factors

Article Snippet: Forty-eight hours after seeding cells, medium was changed to include 10 mM of one small molecule from the epigenetic library (Selleckchem, L1900) or an equal volume of H2O or DMSO as negative controls and 50 ng/mL of Fgf7 as a positive control.

Techniques:

Journal: Frontiers in Oncology

Article Title: PBRM1 Deficiency Sensitizes Renal Cancer Cells to DNMT Inhibitor 5-Fluoro-2’-Deoxycytidine

doi: 10.3389/fonc.2022.870229

Figure Lengend Snippet: Epigenetic compound library screen identifies DNMT inhibitors as synthetic lethal drugs in PBRM1-deficient renal cancer cells. (A) Western Blot analysis showing loss of PBRM1 expression in the three PBRM1−/− clones. (B) The genomic Sanger sequencing of PBRM1 locus in 786-O PBRM1+/+ and PBRM1-/-(#1) cells. PBRM1−/− clone#1 lost 25 nucleotides in exon 3. (C) A compound inhibition rate plot of the first round screen data are shown. (D) A log10-IC50 plot of the second round screen data are shown. The IC50 values of the compounds against 786-O PBRM1+/+ and PBRM1-/- cells was plotted. Compounds with selectivity index (SI) > 2 for PBRM1−/− cells were chosen as synthetic lethality candidates. (E–H) Cell viability assay was done to certify the synthetic lethality effect by Fdcyd in 786-O isogenic pairs (E) and CAKI-1 isogenic pairs (F) . The other two DNMTis 5-Azacytidine (G) and Decitabine (H) were also used to test the IC50 in 786-O isogenic pairs. Error bars represent s.d. (n = 9) from three independent experiments. ANOVA P value of <0.001 for Fdcyd, 5-Azacytidine and Decitabine.

Article Snippet: Epigenetics Compound Library (L1200, 773 epigenetics compounds) was purchased from Topscience.

Techniques: Drug discovery, Western Blot, Expressing, Clone Assay, Sequencing, Inhibition, Viability Assay

Journal: Frontiers in Neuroscience

Article Title: Selected Histone Deacetylase Inhibitors Reverse the Frataxin Transcriptional Defect in a Novel Friedreich’s Ataxia Induced Pluripotent Stem Cell-Derived Neuronal Reporter System

doi: 10.3389/fnins.2022.836476

Figure Lengend Snippet: Screening of epigenetic compound library to identify novel inducers of FXN expression. (A) An overview of the screening process. All compounds of the APExBIO DiscoveryProbe™ Epigenetics Compound Library were tested at 10 μM concentration. Luminescence signal was plotted independently per each plate. The green line corresponds to plate average signal; dashed lines indicate average signal plus 1, 2, and 3 standard deviations of the mean. All data from two rounds of screening are included as . (B) Secondary validation of the efficacy of 16 compounds selected by initial screens. Luminescence detection was performed after 24 and 48 h of treatment. DMSO- and RG109-treated FXN-NLuc NPCs were used as controls. Five compounds were selected for further studies: CI994, Mocetinostat, Entinostat, UF 010, and Cerdulatinib. Results are mean ± SD from three technical replicates; * indicates p < 0.05 by one-way ANOVA. (C) Dose–response analyses for the selected compounds. Luminescence analyses were performed after 48 h of treatment with compounds at 0.5, 1, 2, 5, and 10 μM. EC50 is indicated for each compound. (D) Determination of cytotoxicity in FXN-NLuc NPCs using an LDH assay. Cytotoxicity is calculated relative to the spontaneous LDH release detected in DMSO-treated cells. Cells were treated with 10 μM of each compound for 48 h. Pirarubicin served as a positive control for cytotoxicity. Results are mean ± SD from three independent experiments; *** indicates p < 0.001 by one-way ANOVA.

Article Snippet: Next, as a proof of concept, we performed a luciferase-based screening of the Discovery Probe Epigenetic Compound Library (APExBIO) that includes 281 compounds predominantly targeting various epigenetic and chromatin pathways ( ).

Techniques: Drug discovery, Expressing, Concentration Assay, Biomarker Discovery, Lactate Dehydrogenase Assay, Positive Control