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12 protocols using ceapin a7

1

Modulating ER Stress Pathways

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PFOA (96%), Thapsigargin (TG), Ionomycin (ION), Thiazolyl Blue Tetrazolium Bromide, Ceapin-A7, 4-Phenylbutyric acid (4-PB), N-acetyl-L-cysteine (NAC), 4,5-Dihydroxy-1,3-benzenedisulfonic acid disodium salt monohydrate (Tiron), Hydrogen peroxide (30%), 2-aminoethoxydiphenyl borate (2-APB) and Dantrolene (Dan) were purchased from Sigma-Aldrich (St. Louis, MO). PERK Inhibitor I (GSK2606414), PERK Inhibitor II (GSK2656157), IRE1 Inhibitor III (4µ8c), and IRE1 Inhibitor IV (KIRA6) were purchased from Millipore Sigma (Burlington, MA). Tunicamycin (TM) was purchased from Santa Cruz Biotechnology (Dallas, TX) and Palmitoleic acid (POA) was purchased from Cayman Chemical (Ann Arbor, MI). Cell culture media and antibiotics were purchased from Sigma-Aldrich (St. Louis, MO) and fetal bovine serum (FBS) was purchased from Hyclone Laboratories (Logan, UT). The following primary antibodies were used for Western analysis: phospho-eIF2α (3597) and Chop (2895) from Cell Signaling Technology (Danvers, MA); eIF2α (sc-133132) and Gapdh (sc-365062) from Santa Cruz Biotechnology (Dallas, TX); and Atf4 (10835-1-AP) from Proteintech Group (Rosemont, IL). Secondary antibodies against mouse or rabbit species were conjugated to HRP and obtained from Cell Signaling Technology (Danvers, MA).
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2

ZFAS1 Expression and Cell Proliferation Assay

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The RNeasy Kit, RT2 First Strand Kit, RT2 SYBR Green ROX qPCR Mastermix, and RT2 lncRNA qPCR Assay for Human ZFAS1 were purchased from Qiagen (Valencia, CA, USA). The BrdU Cell Proliferation Assay Kit was purchased from BioVision (Mountain View, CA, USA). The sorafenib was purchased from LC Laboratories (Woburn, MA, USA). The GSK-2606414 was purchased from APExBIO (Boston, MA, USA). The trans-ISRIB was purchased from Tocris Bioscience (Ellisville, MO, USA). Ceapin-A7 and 4μ8c were purchased from Sigma-Aldrich (St. Louis, MO, USA). Silencer Select pre-designed siRNA for human ZFAS1, negative control siRNA, and RNAiMAX transfection reagent were purchased from Thermo Fisher Scientific (Wilmington, DE, USA).
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3

Investigating ER Stress Pathways in PEL Cells

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BC3 (ATCC, CRL-2277) and BCBL1 (kindly provided by Prof. P. Monini, National AIDS Center, Istituto Superiore di Sanità, Rome, Italy) are human B-cell lines derived from Primary effusion Lymphoma (PEL). Cells were cultured in RPMI 1640 (Sigma-Aldrich, St. Louis, MO, USA, R0883) with 10% fetal calf serum (Euroclone, Milano, Italy, ECLS0180L), l-glutamine (2 mM) streptomycin (100 µg/mL) and penicillin (100 U/mL) (Gibco, Gaithersburg, MD, USA, 10378-016) in 5% CO2 at 37 °C. Cells were treated with the following drugs: 4μ8C (IRE1 RNAse inhibitor) provided by Sigma (Sigma-Aldrich, MO, USA, cat n. SML0949), Ceapin-A7 (ATF6a signaling blocker) provided by Sigma-Aldrich (cat n. SML2330), GSK2606414 (PERK inhibitor) provided by Selleckem, USA (cat. n. S7307). Chloroquine (CQ) (inhibitor of autophagic protein degradation) (Sigma-Aldrich, MO, USA, cat. n. C6628). Chemicals were added to cell cultures at the final concentrations of 10 and 20 μM (4μ8C), 6 and 12 μM (Ceapin) and 10 and 20 ng/mL (GSK2606414) for 24 h; Cloroquine was used at final concentration of 10 μM for 18 h. After treatments, cells were collected, counted by trypan blue exclusion assay using a hemocytometer and used for further analysis. Each experiment was performed in triplicate and repeated at least three times.
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4

Characterizing Inhibitors of ER Stress

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AA147 and AA263 were described in previous publications [23 (link)]. Ceapin-A7 (#SML2330) and apyrase (#A6237) were obtained from Sigma. PF429242 (#15,140) and 4μ8c (#22,110) were obtained from Cayman Chemical. DMSO (0.1% v/v final concentration) was used as a vehicle control, which matches its concentration in AA147 and AA263.
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5

Culturing and Treating Mouse Embryonic Fibroblasts

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Mouse embryonic fibroblast (MEF) cells were kindly provided by Dr. Randal J. Kaufman. Cells were maintained in DMEM (Corning, Corning city, NY, USA) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (FBS, Corning) and 1% (v/v) penicillin and streptomycin (P/S, Corning) at 37 °C in an incubator with 5% CO2. Cells were treated with thapsigargin (TG; Sigma Aldrich, St. Louis, MO, USA), 4μ8c (Cayman, Ann Arbor, MI, USA, 22110), or ceapinA7 (Sigma Aldrich) at the indicated concentrations and time points. MEFs expressing Fv2E-PERK were treated with AP20187 (B/B homodimerizer; Takara, Kusatsu, Shiga, Japan) at the indicated concentrations and time points.
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6

Antibody and Small Molecule Profiling for ER Stress Response

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Antibodies including HT-7 (catalog no.: MN1000; Invitrogen), AT8 (catalog no.: MN1020; Invitrogen), YFP (catalog no.: ab6556; Abcam), HSP90 (catalog no.: ab13492; Abcam), lamin A/C (catalog no.: 2032; Cell Signaling Technology), GAPDH (catalog no.: ab8245; Abcam), T-PERK (catalog no.: 3192; Cell Signaling Technology), phosphorylated PERK (catalog no.: 3179; Cell Signaling Technology), eIF2α (catalog no.: 5324; Cell Signaling Technology), p-eIF2α (catalog no.: 5324; Cell Signaling Technology) were pretested to detect the targeted proteins. Small molecules included GSK2656157 (catalog no.: 9466-5; BioVision), GSK2606414 (catalog no.: S7307; Selleckchem), salubrinal (catalog no.: S2923; Selleckchem), ISRIB (catalog no.: S7400; Selleckchem); Ceapin-A7 (catalog no.: SML2330; Sigma–Aldrich), 4u8C (catalog no.: CAS14003-96-4; Calbiochem), and AA147 (product no.: 6538059; ChemBridge) were prepared in dimethyl sulfoxide following the manufacturer’s instruction and stored at −80 °C as stock solution. ER stress–inducing chemical, thapsigargin, was dissolved in dimethyl sulfoxide and added to the cell culture media at a concentration of 300 nM. The working solutions were freshly prepared with −80 °C stock solution.
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7

Synthesis and Verification of Prostamide Derivatives

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15-deoxy, Δ12,14-prostamide J2 and 9,10-dihydro-prostamide J2 were synthesized, and their identity and purity were verified according to our previously published methods [25 (link)]. GSK2606414, STF083, Ceapin-A7, salubrinal, thapsigargin, 4-phenylbutyric acid, 2-aminoethoxydiphenyl borate, cyclosporin A and ruthenium red were purchased from Sigma-Aldrich (St. Louis, MO, USA). Caspase-Glo® 3/7 and MTS reagent were from Promega Life Sciences (Madison, WI, USA).
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8

Wound Healing Assay with Drug Treatment

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Cells were inoculated into 6-well plates after centrifugation and digestion with 0.25% trypsin. When the cell density reached up to 90% or more, 3 vertical lines were scratched in each well with a 10 µL pipette tip and the floating cells were gently washed away with 1× PBS. Complete medium was added, and a photo was taken of the scratches at 0 h. Three different fields of view were selected for each well for photography. After photography, the medium was changed to a serum-free medium. The healing of the wound was photographed at the same location at the corresponding time of 24 h, 48 h and 72 h after incubation. The experiment was repeated 3 times. To observe the healing effect of drugs on the cell wound, the corresponding drugs (Tunicamycin 0.5 μg/mL, Sigma, T7765; GSK621 30 μM, MCE, HY-100548; CeapinA7 16 μM, Sigma, 2323027-38-7) were added into the serum-free medium. Afterwards, the wound healing was observed under the microscope at 0 h, 24 h, 48 h and 72 h and analyzed using ImageJ software.
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9

Plasmacytoid dendritic cell activation

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Sorted bone marrow-pDCs were aliquoted into 96 well plates at 100,000 cells per well. Cells were stimulated with 1 mM of CpG A (ODN1585) or B (ODN1886) for 24 h, unless otherwise stated. For the pharmacological inhibition of the ATF6 pathway, cells were treated with AEBSF at a final concentration of 100 µM or with Ceapin A7 (Sigma) at a concentration of 3 µM, four hours post stimulation with CpG ODN. For co-culture experiments 100,000 CD19-positive wild type B cells, purified by a positive MACs selection, were co-cultured with 30,000 FACS-sorted bone marrow-derived pDCs and stimulated with 1 mM CpG C (ODN M362) and anti-IgM for 72 h as previously described in50 (link). All ODNs used were obtained from Invivogen.
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10

Modulation of Lipid Metabolism Pathways

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TAG formation was inhibited using the DGAT1 inhibitor T863 (MedChemExpress, #HY-32219) and the DGAT2 inhibitor PF 06424439 (Bio-Techne, #6348/5). Import of fatty acids into mitochondria was blocked by CPT1 inhibitor etomoxir (Calbiochem, #236020). Desaturation of fatty acids was inhibited by the SCD1 inhibitor CAY10566 (MedChemExpress, #HY-15823-1mg). Lipolysis was inhibited by treating the cells with the ATGL inhibitor atglistatin (Sigma-Aldrich, #SML1075). The ER stress response branches were inhibited individually using the PERK inhibitor GSK2606414 (MedChemExpress, #HY-18072), the IRE1a inhibitor GSK2850163 (Sigma-Aldrich, #1684), and the ATF6 inhibitor Ceapin-A7 (Sigma-Aldrich, #SML2330). ER stress was chemically induced with tunicamycin (Sigma-Aldrich, #5045700001) and thapsigargin (Sigma-Aldrich, #586005). Autophagosome-lysosome fusion was blocked using the V-ATPase inhibitor bafilomycin A1 (VWR, #J61835.MX). The concentration of each treatment is indicated in the figure legends.
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