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9 protocols using 2 fdg

1

Evaluating Sugar Analog Effects on Cell Death

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iSLK.BAC16 cells were plated at 8000 cells/well in a 96‐well plate in triplicates. The next day all cells, except for the control cells, were induced with DOX (1 µg/ml, Sigma) and sodium butyrate (1 mM) alone or in addition to one of the sugar analogs: 2‐DG (Sigma), 2‐FDG (Carbosynth), or 2‐DFM (Carbosynth) at 5 mM. Additionally, a Cytotox Red Reagent at 250 nM (Essen Bioscience) was added to all wells. Cells were incubated in an Incucyte Zoom (Essen Bioscience) to acquire green and red fluorescence images at 10X magnification every 4 h. The death index was calculated for each data point with the formula: red object count (dead cells)/green object count (iSLK.BAC16 cells).
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2

Monitoring Cell Death via Fluorescence

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iSLK.BAC16 cells were plated at 8,000 cells/well in a 96-well plate in triplicates. The next day all cells, except for the control cells, were induced with doxycycline (1 μg/mL, Sigma) and sodium butyrate (1 mM) alone or in addition to one of the sugar analogs: 2-DG (Sigma), 2-FDG (Carbosynth), or 2-DFM (Carbosynth) at 5 mM. Additionally, a Cytotox Red Reagent at 250 nM (Essen Bioscience) was added to all wells. Cells were incubated in an Incucyte Zoom (Essen Bioscience) to acquire green and red fluorescence images at 10×magnification every 4 hours. The death index was calculated for each data point with the formula: Red object count (dead cells)/Green object count (iSLK.BAC16 cells).
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3

Modulation of KSHV Virion Production

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iSLK.219 cells were induced at 60% confluency with DOX (1 µg/ml, Sigma‐Aldrich) and sodium butyrate (1 mM) in the absence (—) or presence of one of the sugar analogs: 2‐DG (Sigma), 2‐FDG (Carbosynth), and 2‐DFM (Carbosynth) at 2 or 5 mM. After 72 h of induction, cell‐free virus‐containing supernatants were collected and, after a serial dilution, were used to de novo infect HEK‐AD293, which were pretreated for 30 min with 8 µg/ml polybrene (Millipore). A total of 72 h after infection, infectious virion production was measured by counting the GFP + HEK‐AD293 by flow cytometry to determine the 50% tissue culture infective dose (1 GFP(+) AdHEK293 cell = 1 infectious KSHV virion).
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4

Kinetic Analysis of KSHV Virion Production

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iSLK. 219 cells were induced at 60% confluency with doxycycline (1 μg/mL, Sigma) and sodium butyrate (1 mM) in the absence (—) or presence of one of the sugar analogs: 2-DG (Sigma), 2-FDG (Carbosynth), and 2-DFM (Carbosynth) at 2 mM or 5 mM. After 72 hours of induction, cell-free virus-containing supernatants were collected and, after a serial dilution, were used to de novo infect HEK-AD293, which were pre-treated for 30 min with 8 μg/mL polybrene (Millipore). 72 hours after infection, infectious virion production was measured by counting the GFP+ HEK-AD293 by flow cytometry to determine the 50% tissue culture infective dose (TCID50) (1 GFP(+) AdHEK293 cell = 1 infectious KSHV virion).
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5

Salinomycin and Glycolysis Inhibitor Effects

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Salinomycin, 2DG, 2FDG and Saponin, were obtained from Sigma-Aldrich and dissolved in their respective buffers as per required concentrations. Antibodies were obtained from the following sources: Rabbit-anti-LC3b (Sigma Aldrich), murine anti-Actin (Abcam) Rabbit anti-PARP1 cleaved subunit antibody (Millipore). Secondary antibodies anti-rabbit HRP-conjugate and anti-mouse HRP-conjugates were obtained from Sigma-Aldrich.
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6

Endothelial cell culture protocols

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2-DG, 2-FDG, oxamate, Mannose, Tunicamycin and (2’Z, 3’E)-6-Bromoindirubin-3′-oxime (BIO) were purchased from Sigma-Aldrich (St. Louis MO). Brefeldin A was acquired from Calbiochem-EMD Millipore (Billerica, MA). Matrigel was obtained from BD Biosciences (Bedford, MA) and used at 7mg/ml. Human bFGF and VEGF were purchased from R&D Systems (Minneapolis, MN). Human microvascular endothelial cells from lung (HMVEC-L) was purchased from Lonza (Walkersville, MD) in 2007, used only till passage 5 and was authenticated by vendor. EBM-2 basal medium and the EGM2 and EGM2-MV supplements were purchased from Lonza (Walkersville, MD). Human umbilical vein endothelial cells (HUVECs, purchased 3-4 times yearly depending on usage and used till passage 5), MDA-MB-231(purchased in 2007) and HT-29 (purchased in 2012, 2014) were purchased from the ATCC (Manassas, VA) and were authenticated by vendor. For the endothelial cell experiments described below, “Unstimulated ECs” are defined as cells maintained with endothelial basal medium (EBM) with 1% FBS while “stimulated ECs” are cells that were starved overnight (EBM and 1% FBS), and then treated with either bFGF or VEGF (10 ng/ml) the day of the experiment. Endothelial cell media contains 1 gram of glucose per liter (5.5 mM).
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7

Hypoxia Impacts Cell Growth

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Cell line cells in logarithmic growth were cultured at the density of 2 × 105/ml (0.5 ml RPMI1640 containing 3% FCS/well) in tissue culture plate, 24 wells (Becton Dickinson, NJ, USA) under normoxia (21% O2) or hypoxia (1% O2). Then, cell number was estimated at 24 hours and at 48 hours by Particle Analyzer (PA-2000, Erma Inc., Japan). Cell line cells were cultured in the same condition with various concentrations of 2-fluoro-2-deoxy-D-glucose (2-FDG: Sigma #F5006) (2, 5 and 10 mM) or oligomycin (oligo: Sigma #O4876) (0.05, 0.2 and 1 μg/ml) or N-acetyl-L-cysteine (NAC: Sigma #A7250) (0.5 mM). Control culture containing same amount of solvent (H2O for 2-FDG, DMSO for oligo) was done simultaneously. After 24 or 48 hours culture, cell number was estimated by Particle Analyzer.
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8

Metabolic inhibition of host cells

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To inhibit host cell glycolysis, glucose starvation or 2FDG (Sigma) treatment were used. To inhibit host cell oxidative phosphorylation, antimycin A (Sigma) treatment was used. HEp-2 cells were allowed to adhere for 24 hours. For glucose starvation, media was changed to media containing no glucose. For 2FDG and antimycin A treatment, media was changed to media containing 5 mM 2FDG or 3 nM antimycin A respectively. 15 minutes after the media was changed, cells were infected with C. trachomatis or were left un-infected. After 24 hours of infections, FLIM measurements, recovery assays, ATP measurements and immunofluorescence stainings were performed.
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9

Endothelial Cell Culture and Protein Analysis

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2-DG, 2-FDG, oxamate, mannose, and FITC-dextran were purchased from Sigma-Aldrich (St. Louis MO). Matrigel was obtained from BD Biosciences (Bedford, MA) and used in vitro at a 7 mg/mL and in vivo at a ∼20 mg/mL concentration. The growth factors bFGF and VEGF were purchased from R&D Systems (Minneapolis, MN). Human umbilical vein endothelial cells (HUVECs), human microvascular endothelial cells from lung (HMVEC-L), EGM-2 and EGM2-MV medium were purchased from Lonza (Walkersville, MD). EGM-2 and EGM2-MV contain serum and the following growth factors: hEGF, VEGF, hFGF-B, R3-IGF-1. All other cancer cell lines were purchased from the American Type Culture Collection (ATCC). The cells were cultured according to the supplier's instructions. For western blotting, anti-KDEL for GRP78 and GRP94 was purchased from Stressgen, (Ann Arbor, MI), polyclonal anti-CHOP/GADD153 was purchased from Santa Cruz Biotechnology (Santa Cruz, CA), and polyclonal cleaved Caspase-3 antibody was purchased from Cell Signaling (Danvers, MA). For immunohistochemistry CD31 monoclonal antibody was purchased at BD Bioscience (Bedford, MA).
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