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9 protocols using n7505

1

Quantifying TrxR1 Enzymatic Activity

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Enzymatic activity of purified TrxR1 variants was assessed colorimetrically by monitoring NADPH (N7505; Sigma)-dependent reduction of Ellman's reagent (DTNB, D8130; Sigma). A plate reader (Synergy H1 Hybrid Multi-Mode Reader, 11-120-534; BioTek) autodispenser was used to add DTNB (in phosphate buffer) to each well to start the reactions, which included final concentrations of 5 mM DTNB, 300 μM NADPH, and 50 nM (Fig. 3A) or 100 nM (Fig. 7B) TrxR1 in a final volume of 100 μL per well. This reaction was monitored at 412 nm every minute for 50 min. Reactions were performed in triplicate. For all activity assays, error bars display one standard deviation based on at least triplicate experiments. A control lacking the TrxR1 enzyme was conducted in triplicate and has been subtracted from all enzyme assays.
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2

Characterization of CYP3A4 Enzyme Kinetics

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Horse heart Cyt c (C2867, ≥99% (SDS-PAGE)), CYP3A4 isozyme microsomes (C4982, with CPR and Cyt b5, recombinant, expressed in baculovirus-infected insect cells), NADPH (β-Nicotinamide adenine dinucleotide 2-phosphate reduced, tetrasodium salt) (N7505), peroxide assay kit (MAK311), protease inhibitor cocktail (P8340), and endoplasmic reticulum isolation kit (ER0100) were all obtained from Sigma-Aldrich Co., Ltd. 6-week-old BALB/c female mice were bought from Liaoning Changsheng biotechnology co., Ltd. Ritonavir (R126586) was purchased from Shanghai Aladdin Biochemical Technology Co., Ltd. Acetonitrile, nickel chloride hexahydrate (NiCl2.6H2O, sodium hydroxide (NaOH), ethylene glycol, hydrazine hydrate (80%), hydrogen peroxide (H2O2, 30%) were purchased from Beijing chemical Co., Ltd. The PBS buffer (10 mM, NaCl, Na2HPO4.12H2O, NaH2PO4.2H2O, pH = 7.25) were prepared in ultrapure water (18.25 MΩ. cm).
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3

Enzyme Kinetics and Inhibition Assay

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NADH (10107735001, Roche, Basel, Switzerland), NADPH (N7505, Sigma, Darmstadt, Germany), and all enzymes were solved in 100 mM MOPS buffer (pH 7.8) (6979.4, Carl Roth, Karlsruhe, Germany). The enzymes PDH (8646-DH-050, R&D Systems, Minneapolis, MN, USA), CTBP1 (PRO-796, ProSpec, Rehovot, Israel), IDH (I5036, Sigma), GAPDH (G2267, Sigma), G6PDH (10127655001, Roche), LDH (LLDH-RO, Roche), HADH (ENZ-499, ProSpec), and MDH (LMDH-RO, Roche) were incubated in varying concentrations with NADH or NADPH, respectively. For the inhibition of LDH, the small molecule FX11 (427218, Sigma) was solved in DMSO and used in varying concentrations (10 µM, 0.5 mM, and 1 mM). All measurements were performed at room temperature.
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4

Murine Colitis Induction and Analysis

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The following reagents were obtained: ketamine (Dopalen injectable®, Paulínia, Brazil), xylazine (Anasedan injectable®, Paulínia, Brazil), Tween 80 (Synth®, Diadema, SP, Brazil), hexadecyltrimethylammonium bromide (HTAB) (Sigma Aldrich® H5882, Steinheim, Germany), o-dianisidine dihydrochloride (Sigma Aldrich® D3252, Steinheim, Germany), dextran sulphate sodium salt (DSS)—colitis grade (36,000–50,000 MW, cod. 02160110-CF, MP Biomedicals, LLC, Solon, OH, USA), hydrogen peroxide (Synth®), horseradish peroxidase (Sigma Aldrich® P8250, Steinheim, Germany), trichloroacetic acid (TCA) (Sigma Aldrich® T4885, Steinheim, Germany), reduced L-glutathione (Sigma Aldrich® G-4251, Steinheim, Germany), β-nicotinamide adenine dinucleotide 2′-phosphate reduced tetrasodium salt hydrate (NADPH) (Sigma Aldrich® N-7505, Steinheim, Germany), 5,5′-dithiobis (2-nitrobenzoic acid) (DTNB) (Sigma Aldrich® D-8130, Steinheim, Germany), and buffer RIPA (Sigma Aldrich® R0278, Steinheim, Germany). IL-1β mouse, IL-10 mouse, CXCL-MIP-2 mouse, and TNF-α mouse were obtained from R&D Systems®, Inc. (Minneapolis, MN, USA).
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5

Glutathione Measurements in Cell Cultures

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Cells were cultured in the 6-well plate. When the culture reaches 70–80% confluency, cells were treated with L-BSO (20 μM) for 12 hours, or treated with LA (20 mM), hydrogen peroxide (100 μM), PEITC (10 μM), PL (10 μM), Dox (10 μg/ml), or ATO (10 μM) for 4 hours respectively. Cells were rinsed twice with 2 ml ice-cold Ca2+-/Mg2+-free PBS. Cells were collected by tripsinization and lysed in 0.2 ml of ice-cold extraction buffer (0.1% Triton-X and 0.6% sulfosalicylic acid in KPE) followed by 4 cycles of freezing and thawing (1 minute in liquid nitrogen and 2 min in water bath at 37°C). Cell lysate was centrifuged and supernatant was collected for GSH and GSSG measurement according to the method described by Rahman et al.53 (link). The GSH assay is based on the chemical conjugation of GSH with 5,5′-Dithiobis(2-nitrobenzoic acid)[DTNB] (Sigma, D-8130). Total glutathione was measured by firstly reducing oxidized glutathione using glutathione reductase (Sigma, G-3664) and β-NADPH (Sigma, N-7505) followed by conjugation with DTNB. To measure GSSG, GSH was firstly covalently reacted with 2-vinylpyridine (Aldrich, 132292), then GSSG was measured as described above. Pierce® BCA protein assay kit was used for protein determination. All samples were run in triplicates. GSH and GSSG levels were expressed in nmol/mg protein.
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6

NADH and NADPH Preparation Protocol

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NADH (N8129, Sigma-Aldrich,
Dorset,
U.K.) and NADPH (N7505, Sigma-Aldrich, Dorset, U.K.) were made up
fresh on the day of experiment as 1 mM solutions in Milli-Q water
containing 10 mM HEPES (H3375, Sigma-Aldrich, Dorset, U.K.) adjusted
to pH 7.2.
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7

NQO1 Activity Measurement Protocol

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NQO1 activity was assessed by measuring the levels of NAD(P)H via absorbance at 340 nm in a Versamax plate reader (Molecular Devices; San Jose, CA, USA) at 37 °C. The reaction mixture in a final volume of 200 µl contained 50 mM ammonium bicarbonate, 0.1 mg/ml BSA, 2 mM EDTA, 200 µM NAD(P)H as electron donor (Sigma–Aldrich, N7505) and 2 µg of recombinant NQO1 (for final enzyme concentration of 0.5 µM). Positive and negative controls were included by adding 400 µM of the NQO1 known substrate menadione (Sigma–Aldrich, M5625) in the presence or absence of the NQO1 inhibitor dicoumarol at 100 µM, respectively. To assess whether the compounds were substrates of NQO1, 100 µM of the indicated compounds were added instead of menadione in the absence or presence of dicoumarol to measure specific NQO1 activity. Measurements were made every 10 sec for 20 min. For analytical high-performance liquid chromatography with diode array detection (DAD) and electrospray ionization mass spectrometry (HPLC-MS), the in vitro reactions were filtered using Amicon Ultra-0.5 centrifugal filter devices with a 30 kD molecular weight cutoff (Merck-Millipore) applying centrifugation for 10 min at 13,000 × g. 100 µl of flow-through samples were injected on an Agilent/HP 1200 system 6110 mass spectrometer with electrospray ionization (ESI+). Absorbance was monitored at 305 ± 90.
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8

Quantification of NADPH and NADP+ Levels

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NADPH and NADP+ levels in unmodified TF-1 cells or TF-1 cells stably expressing primary and/or second-site IDH mutations were measured using the NADP/NADPH Glo-Assay (Promega, G9081; refs. 58, 59 (link)) following the manufacturer's instructions. After the standard curves were generated using the purified NADPH (Sigma-Aldrich, N7505) and NADP+ (Sigma-Aldrich, N5755) in the same buffer as the experimental samples, the absolute amount of NADPH and NADP+ was obtained for each sample.
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9

Nitrite and Nitrate Quantification in RBCs

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Mouse blood samples used for the EPR analyses were stored at 20–25°C in the dark until subsequent thawing for nitrite/nitrate assay. Human RBCs were collected as described above and used for NO2- and NO3- quantification immediately. Briefly, after hemoglobin precipitation with cold ethanol/chloroform (v: v– 1: 5) and vortex agitation, the mixture was centrifuged at 10,000xg for 10 minutes at 4°C. Aliquots of clear supernatants were used to detect NO2- and NO3-. For nitrite measurements, supernatants were incubated with Griess reagents according to Griess Reagent Kit instructions (G-7921, ThermoFisher). The nitrite concentrations were determined using a calibration curve (1–100 μmol/L) of sodium nitrite in deionized water. For nitrate measurements, NO3- was first reduced to NO2- in presence of NADPH 80 μmol/L (N-7505, Sigma) and nitrate reductase 50mU / 100 μl (N-7205, Sigma). The resulting total concentrations of nitrite and nitrate in samples (including products formed after NO oxidation) were determined by comparison with a calibration curve (1–100 μmol/L of sodium nitrite in deionized water). The nitrate concentrations were determined by the difference between the total NO oxidation products and nitrite concentrations from the same aliquots. Measurements of the absorbance at 548 nm were performed with a Spectramax i3 (Molecular Devices, LLS, USA).
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