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9 protocols using unc0638

1

Cortisol and IL-6 Regulation of H3K9 Methylation

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The Caco-2/BBE (American Type Culture Collection, Manassas, VA) epithelial cells were maintained at 37°C in 10% CO2. Cells underwent differentiation for 21 days with medium changes every three days. Cells were then incubated with cortisol (500 nM; Cayman Chemical) or IL-6 (10 ng/ml) for 24 hours ± the H3K9 methylation inhibitor UNC0638 (500 nM; Cayman Chemical) that inhibits G9a and GLP catalyzing H3K9me and H3K9me235 (link),37 (link) and BRD4770 (10 μM; Cayman Chemical) that inhibits G9a and selectively reduces H3K9me2 and H3K9me3. DMSO at the final 0.01% (v/v) concentration was used as the vehicle control.
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2

In Vitro Cell Stimulation and Maintenance

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For the in vitro cell stimulation and maintenance, the following reagents were used: human IL-2 (Roche); IL-21 (PeproTech); goat antihuman F(ab′)2 fragments (anti-IgM & IgG) (Jackson ImmunoResearch); lipid mixture 1 chemically defined (200×) and MEM Amino Acids Solution (50×) (Sigma-Aldrich); for G9A inhibition, UNC0638 (Cayman Chemical); and for cell proliferation: CFSE (Sigma-Aldrich).
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3

Drug Synergy Evaluation in Brain Tumors

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DAOY, UW228, DAOY-HR vs DAOY-LR and UW426-HR vs UW426-LR cells were cultured in 96-well microplates and treated with various concentration of the AKT inhibitor MK2206 (US Biological Life Science), HDAC inhibitor MS275 (Cayman Chemicals, catalog # 13284) and G9a inhibitor UNC0638 (Cayman Chemicals, catalog # 10734), either alone or in combination for the time period indicated in the figures. After labeling with 3-(4,5-Dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT/thiazolyl blue tetrazolium bromide; Sigma), cell growth was analyzed by SpectraMax Plus 384 microplate reader (Molecular Devices, LLC). Synergy between MS275 and UNC0638 was calculated using the fractional product method of Webb using the formula g1g2 = g12 following the procedure described previously (80 (link)).
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4

Stem Cell Chemical Library Screening

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The Stem Cell Chemical Library was assembled from commercially available compounds, and diluted to a stock of 10 mM in DMSO. Chemicals were further diluted to 20 µM in DMEM before being added to the cells. The chemicals used are listed in Table 1. UNC0638 was purchased from Cayman Chemical and diluted to a stock of 10 mM in DMSO for all cell culture experiments. JIB-04 was purchased from Tocris was diluted to a stock of 10 mM in DMSO for cell culture experiments and 5.5 mg/ml in Koliphor-EL (Sigma) for mouse experiments. Pemetrexed was purchased from the Dana Faber Cancer Center and was diluted to a stock of 100 mM in ddH2O. For cell culture experiments, cells were grown in the presence of the drug for 96 h with fresh media and drugs were supplied at 48 h.
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5

Evaluating Cytotoxic Effects of E67 and UNC 0638

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E67 was synthesized in accordance to the methods described by Chang et al (22 (link)). UNC 0638 was purchased from the Cayman Chemical Company (Ann Arbor, MI) (23 (link)). Both drugs were dissolved in DMSO and stored at −20°C. DAOY, DAOY-REST cells (3×104), UW426 (4×104) and D283 (7.5×104) were seeded at the indicated densities in 96-well plates containing 100 μl of media. After overnight incubation, cells were treated for 24, 48, 72 hrs with E67, UNC 0638 or DMSO at concentrations ranging from 0.125 μM-10 μM and 0.125 μM -4 μM, respectively. MTT assays were performed as described previously (5 (link),7 (link),24 (link)). Absorbance at 570 nm and background at 650 nm were read on a multiwell spectrophotometer. Results were expressed as a percentage (%) of the control (DMSO).
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6

Epigenetic regulators in pancreatic cells

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Pancreatic cell lines were grown in Dulbecco’s modified Eagles medium containing 10% fetal bovine serum (FBS). RNA interference expression plasmids specific for G9a, KDM7A and PCL3 were purchased from the National RNAi Core Facility (Academia Sinica, Taiwan). The sources of antibodies are: G9a from Epitommics (Burlingame, CA); E-cadherin and EZH2 from BD (San Jose, CA); H3K9m2, H3K9m3, H3K27m2, H3K27m3, H3K4m2 and H3K4m3 were from Cell Signalling (Danvers, MA); KDM7A, MLL1 and SETD1A were from Abcam (Cambridge, MA). PCL3 and FLAG were from Sigma-Aldrich (St. Louis, MO). UNC0638 was purchased from Cayman Chemical (Ann Arbor, MI). KDM7A expression plasmid was kindly provided from Dr. Masabumi Shibuya (Jobu University, Japan).
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7

Investigating Epigenetic Modulators

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Reagents used were as follows: LPS (Escherichia coli O111:B4, Sigma Aldrich); GSK 343, MI-2 (hydrochloride), UNC0638 and Torin 1 (Cayman Chemical, Ann Arbor, MI); MTA (5’-Deoxy-5’-(methylthio)adenosine) and pargyline (Sigma Aldrich); EGCG ((-)-Epigallocatechin gallate) and givinostat (ITF2357) (Selleck Chemicals, Houston, TX).
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8

Evaluating DNA Damage Repair Modulation

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All cells were cultured in DMEM supplemented with 10% FBS and 1% antibiotic-antimycotic agent (Life Technologies, USA). The HeLa DR-GFP cells were provided by Dr Maria Jasin (Memorial Sloan Kettering Cancer Center). For chemical treatments, cells were incubated with 2.5 μM of MS-275 (Focus Biomolecules, USA), 2.5 nM of FK228 (TOCRIS Bioscience, UK), 3 μM of UNC0638 (Cayman Chemicals, USA) or the indicated doses of olaparib (JS Research Chemical Trading, Germany) for 24 h unless otherwise indicated. For IR, cells were exposed to X-ray irradiation (10 Gy) and further cultured for 1 h before indirect immunofluorescence unless otherwise indicated.
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9

Lung Adenocarcinoma Cell Lines Protocol

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Two human RAS mutated non-small cell lung adenocarcinoma cell lines were used in this study. Both cell lines were purchased from American Type Culture Collection (ATCC, USA). All of these cell lines were authenticated by Integrative Genomics Core by using short tandem repeat polymorphism analysis. H1299 (p53-Null, N-RAS mutation) was cultured in RPMI 1640 (ATCC, USA) medium and A549 (p53-Wild-type, K-RAS mutation) was cultured with DMEM/F12 (Corning, USA) medium. For all cell lines, cell authentic growth medium was supplemented with 10% FBS, 100 U/mL penicillin and 100 mg/mL streptomycin. Cell lines were tested Mycoplasma free using colorimetric mycoplasma detection assay with HEK-Blue™-2 cells. Cells used for experiments were within 20 passages from thawing. UNC0638, a selective inhibitor for G9a and GLP methyltransferase, was purchased from Cayman Chemical Company (USA) and used at a concentration of 2.5 μM and 5 μM. Defactinib hydrochloride, a FAK inhibitor which inhibits FAK phosphorylation at Tyr397, was purchased from MedChemExpress (USA) and used at a concentration of 1μM. Parthenilide, NF-κB inhibitor, was purchased from Abcam and used at a concentration of 20 μM.
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