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7 protocols using c2 ceramide

1

ER Stress Modulation of Cell Cycle

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Cells were treated with Tm (Calbiochem) at a final concentration of 1 µg/ml at 30°C for 3 h to analyze cER inheritance and 2 h to analyze septin, unless otherwise noted. Using α-factor–synchronized cells, we have previously shown that cER inheritance and cytokinesis are effectively blocked when Tm is added to small-budded cells before cER inheritance. If cells experience ER stress after cER stably enters into the daughter cell, such cells will divide once, and then cER inheritance and cytokinesis will be blocked in the next round of the cell cycle. A 3-h treatment is sufficient to block ER inheritance in daughter cells, regardless of cell cycle stage (Piña and Niwa, 2015 (link)). Myriocin was stored as a stock 200-µM solution in methanol and used at 400 ng/ml. AbA was stored as a stock 2-mg/ml solution in DMSO and used at 50 ng/ml. Myriocin was added to cells 30 min before Tm. AbA was added to the cells at the same time as Tm. PHS (Sigma), C2-DHC (Enzo Life Sciences), and C2-ceramide (Enzo life sciences) were stored as stock 10-mM solutions in DMSO and used at 1, 5, and 20 µM. PHS-, DHC-, and ceramide-treated cells were grown in SC with 1 M sorbitol at 30°C.
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2

Calcium Signaling Pathway Analysis

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The primary antibodies used in this study and their working concentration were listed in Supplementary Table 2. Thapsigargin (TG, an endoplasmic reticular Ca2+-ATPase inhibitor) was purchased from Sigma-Aldrich (St. Louis, MO, USA). C2-ceramide was purchased from Enzo Life Sciences (USA)
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3

Rat Cortical Neuron Apoptosis Assay

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Embryonal rat cortical neurons (RCN) were derived as previously described from rat E15-16 cortices35 (link). For each experiment, cortices were obtained from all embryos (mixed, unknown sex) of a single pregnant Sprague-Dawley® dam (Envigo). After dissociation, cells were seeded onto 96-well, 12-well, 60 mm, 100 mm cell culture plates (Corning, Corning, NY) or XF24 cell culture microplates (Agilent, Santa Clara, CA) and maintained in serum-free conditions using the B27 supplement (ThermoFisher, Waltham, MA) as described previously35 (link). We previously showed these cultures are >90% neuronal36 .
Etoposide (Cat. #BML-GR307, Enzo Life Sciences, Farmingdale, NY), staurosporine (Cat. #ALX-380-014, Enzo Life Sciences, Farmingdale, NY), camptothecin (Cat. #ALX-350-015, Enzo Life Sciences, Farmingdale, NY), C2-ceramide (Cat. #BML-SL100, Enzo Life Sciences, Farmingdale, NY), doxorubicin (Cat. #CST-5927, Cell Signaling Technologies, Danvers, MA), and mithramycin (Cat. #11434, Cayman Chemical Company, Ann Arbor, MI) were used to treat 7 days in vitro (DIV) cells at concentrations and for times indicated elsewhere.
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4

Ceramide-Induced Cell Death Mechanisms in SH-SY5Y Cells

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SH-SY5Y cells were treated with cell-permeable, biologically active ceramide, C2-ceramide, at a 10 to 50 μM concentration for various times up to 24 h. In most of the experiments, the cells were treated with the following compounds: PJ-34 (20 μM), PARP-1 inhibitor; α-pifithrin (20 μM), p53 inhibitor; cyclosporine A (2 μM), inhibitor of the permeability transition pore; UO126 (1 μM), ERK1/2 kinase inhibitor; SP600125 (5 μM), JNK kinase inhibitor; sphingosine-1-phosphate (1 μM), LY294002 (50 μM), PI3-K inhibitor and Z-DEVD-FMK (100 μM), caspase-3 inhibitor added 1 h before incubation with C2-ceramide (25 μM). Our data showed that most of these compounds had no effect on cell viability in the control condition, with the exception of PARP-1 inhibitor, JNK kinase inhibitor and PI3-K inhibitor, which significantly decreased SH-SY5Y cell survival (by about 20 %, PJ-34, SP600125; 35 %, LY294002). The above-mentioned compounds were purchased from the following: C2-ceramide and sphingosine-1-phosphate from Enzo Life Sciences, LY294002 from Cell Signalling Technology, PJ-34, α-pifithrin, SP600125, U0126 and cyclosporine A from Sigma-Aldrich, Z-DEVD-FMK from Tocris Bioscence.
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5

Evaluating Cellular Stress Responses

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C2 Ceramide, 4 HPR (fenretinide), fumonosin and TGF-β1 were obtained from Enzo Life Sciences, Farmingdale, NY. CTGF ELISA kit was purchased from Antigenix America Inc. Huntington Station, NY. Fetal bovine serum and all other cell culture media were obtained from Laguna Scientific, Laguna Niguel, CA. SYBR Green PCR master mix, gene-specific primers for CTGF and GAPDH were purchased from Roche Inc.-and Valuegene Inc, San Diego.
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6

Lipid Metabolism Regulation Pathway

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Tissue culture medium was from Gibco. [γ-32P]ATP was purchased from PerkinElmer. Palmitate, fatty-acid-free BSA, MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide], ethylene-diamine-tetra-acetic acid (EDTA), disodium salt, perchloric acid, hydrogen chloride, Anti-HA (hemagglutinin), SPT2 antibodies, and insulin human solution were from Sigma–Aldrich. Myriocin, l-cycloserine, D609, C2-ceramide, C2-dihydroceramides, and N-butyldeoxynojirimycin were from Enzo Life Sciences. Ro31-8220 and DAG kinase were from Calbiochem. All solvents were from Merck Eurolab or Fisher Scientific. phospho-Akt (Thr 308), phospho-Akt (Ser 473), Akt, p-PKCζ (Thr 410-403), PKCζ, and β-actin antibodies were from Cell Signaling. Ultrapure water was obtained with a Milli-Q system (Millipore, Bedford, MA, USA). Adenoviruses containing the cDNA of GFP, wild-type PKCζ (WT- PKC), constitutive active PKCζ (CA-PKCζ), or kinase-dead PKCζ (KD-PKCζ) were prepared as previously described [14] (link). All PKCζ constructs contained an HA tag for monitoring their expression.
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7

Characterizing Protein Trafficking Mechanisms

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Rabbit polyclonal anti-myc antibody, mouse monoclonal anti-actinin-1 antibody, and DMSO were from Sigma–Aldrich (St Louis, MO, USA). Mouse monoclonal anti-Stx6 antibody was from BD Transduction Laboratories (San Jose, CA, USA). Rabbit polyclonal anti-Stx6 and anti-Stx16 antibodies were from Synaptic Systems (Goettingen, Germany). Mouse monoclonal anti-Tubulin antibody was from Abcam (Cambridge, MA, USA). Human holo-transferrin conjugated to A488 was from Invitrogen (Grand Island, NY, USA). Mouse anti-myc (c-Myc 9E10) and rabbit anti-furin (H-220) were from Santa Cruz Biotechnology (Dallas, TX, USA). Polyclonal anti-P-Akt(308) and P-Akt(473) were obtained from Cell Signaling Technology (Danvers, MA, USA). Cy3- and A488-conjugated donkey anti-rabbit and donkey anti-mouse secondary antibodies and horseradish peroxidase (HRP)-conjugated goat anti-rabbit secondary antibodies were purchased from Jackson ImmunoResearch Laboratories (West Grove, PA, USA). Nocodazole was purchased from EMD Biosciences Inc. (Darmstadt, Germany) (10 mM stock in DMSO) and C2-ceramide was purchased from Enzo Life Sciences (Farmingdale, NY, USA) (50 mM stock in DMSO). Pre-designed siRNA for Stx6 (siStx6: 5′-CCGAGTCATCAGAAGAACTAA-3′) and non-related (siNR: 5′-AATAAGGCTATGAAGAGATA C-3′) were from Qiagen (Valencia, CA, USA). Human insulin was purchased from Eli Lilly (Indianapolis, IN, USA).
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