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5 protocols using oligomycin

1

Comprehensive Compound Acquisition Protocol

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Sorafenib (#T0093L) was purchased from TargetMol (Shanghai, China); lenvatinib (#S1164), brivanib (#S1084) and bafilomycin A1 (#S1413) were purchased from Selleck (Shanghai, China); cisplatin (#P4394), doxorubicin (#D1515), N-acetyl-l-cysteine (NAC, #A7250), and Hoechst (#94403) were purchased from Sigma‒Aldrich (Shanghai, China); canagliflozin (#A11100) was purchased from AdooQ Bioscience (Nanjing, China); and oligomycin (#HY-N6782), antimycin A (#HY-105755), phloretin (#HY-N0142), z-VAD-FMK (#HY-16658B), necrostatin-1 (#HY-15760), and ferrostatin-1 (#HY-100579) were purchased from MedChemExpress (Shanghai, China).
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2

Metabolic Flux Analysis of Cells

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The extracellular acidification rate (ECAR) and oxygen consumption rate (OCR) were measured using the Seahorse XFe24 extracellular flux analyzer (Agilent Technologies, USA), in accordance with the guidelines included in the manufacturer's protocol. The cells were plated on an XFe24 plate at a density of 2×104 cells/well, and then incubated for the whole night. One hour prior to the assay, the media were replaced with XF media. To conduct the ECAR assay, XF media was used to dilute Glucose (Sigma, G7021), Oligomycin (MedChemExpress, HY-N6782), and 2-deoxy glucose (2-DG; Sigma, D8375). The cartridge was subsequently filled with these diluted chemicals at concentrations of 10 mM, 1 μM, and 50 mM, in that order. Oligomycin, FCCP (Absin, abs816229), Antimycin A (Biovision, 2247), and Rotenone (MedChemExpress, HY-B1766) were diluted in XF medium in order to conduct the OCR test. The cartridge was then filled with these diluted substances at concentrations of 1 μM, 2 μM, 0.5 μM, and 0.5 μM, in that order.
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3

Gastric Cancer Cell Line Maintenance and Inhibitor Treatment

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Human GC cell lines (MKN-45, MKN-28, MGC-803, AGS, and HGC-27), the normal gastric epithelial cell line GES-1, and HEK293T cells were acquired from Shanghai Cell Bank Type Culture Collection Committee (CBTCCC, Shanghai, China) and maintained at 37 °C with 5% CO2. All cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (HyClone, Logan, USA) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin, and 100 μg/ml streptomycin (Invitrogen). Stable cell lines were treated with selected inhibitors, maintained at 37 °C, and harvested at the indicated time points for subsequent analysis. All the cell lines were recently authenticated by short tandem repeat analysis. The proteasome inhibitor cycloheximide (CHX) and the HK2 inhibitor 2-deoxy-d-glucose (2-DG) were purchased from Sigma‒Aldrich (Germany). Ribosomal RNA synthesis inhibitor CX-5461 and oligomycin were purchased from MedChemExpress Company (USA).
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4

Anti-inflammatory Compound Norbergenin Protocol

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Norbergenin (purity ≥ 98%) was obtained from Baoji Herbest Company (Baoji Herbest Bio-Tech Co., Ltd, Shanxi, China), LPS from Escherichia coli 055:B5 (Cat: L2880), Antimycin A (Cat: A8674), sodium pyruvate (Cat: 11360039), D-(+)-Glucose (Cat: G7021), D-glutamine (Cat: 158968) and 2-Deoxy-D-glucose (2-DG, Cat: D8375) were purchased from Sigma-Aldrich. SB203580 (Cat: HY-10256), U0126 (Cat: HY-12031), SP600125 (Cat: HY-12041), oligomycin (Cat: HY-N6782), rotenone (Cat: HY-B1756), FCCP (Cat: HY-50202), methylthiazolyldiphenyl-tetrazolium bromide (MTT) (Cat: HY15924) were obtained from MedChemExpress. Griess Reagent System (Cat: G2930) was obtained from Promega Corporation. Transfer membrane Immubilon-P PVDF (Cat: IPVH00010) was obtained from Millipore. All other reagents were of analytical grade and obtained from Sigma.
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5

Oxidative stress response in 661w cells

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661w cells were purchased and validated from Aolu Biotechnology (Shanghai, China). The cells were cultured in high-glucose Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin, and 100 μg/ml streptomycin. Cultures were maintained at 37 °C in a humidified atmosphere of 95% air and 5% CO2. After the cell confluence reached 80%, the cells were treated with 0–10 mmol/L hydrogen peroxide (H2O2; Amresco, OH, USA, Cat#E882). For the group treated with 1 mmol/L nicotinamide riboside (NR; Yuanye, Shanghai, China, Cat#S31692) or 10 μmol/L doxycycline (DOX; MedChem Express, NJ, USA, Cat#HY-N0565B) and H2O2, the cells were pretreated with NR or DOX for 24 h, then incubated with H2O2 for additional 12 h. For the group treated with 50 μmol/L chloroquine (CQ; MedChem Express, Cat#HY-17589) or 1 μmol/L cyclosporine (CsA; MedChem Express, Cat#HY-B0579), the cells were pretreated with CQ or CsA for 2 h before NR treatment. Incubation of 10 μg/mL oligomycin (MedChem Express, Cat#HY-N6782) and 1 μmol/L antimycin A (GLPBIO, CA, USA, Cat#GC42818) for 6 h was used as a positive control of mitophagy. NR, CsA, oligomycin, and antimycin A were dissolved in dimethysulfoxide (DMSO), while DOX and CQ were dissolved in distilled water. All the drugs were further diluted in the cell culture medium to achieve their working concentrations.
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