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17 protocols using dimethyl 2 oxoglutarate

1

Metabolic Regulation of Peritoneal Macrophages

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Peritoneal macrophages were stimulated with MLE-12 or LLC Exo. (40μg/mL) for 16 hours. Cells were then washed and incubated in glucose free RPMI for 30 minutes before 2-NBDG (400μM, BioVision) was added. Cells were incubated with 2-NBDG for 15 minutes before washing and staining with viability dye and F4/80 for analysis via flow cytometry. The following concentrations of metabolic inhibitors or substrates were used for 16-hour cell culture: 2-deoxy-D-glucose (1mM, Sigma), SEITU (2–4mM, Cayman Chemical), Dimethyl-2-oxoglutarate (1mM-5mM, Sigma), Sodium-L-Lactate (20mM, Sigma), AZD3965 (250nM, MedChemExpress). Levels of L-lactate in the supernatants were measured by L-Lactate Assay Kit I (Eton Bioscience, San Diego, CA) according to manufacturer’s instructions.
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2

Metabolite Analysis of Cell Lines

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Supplier and catalogue numbers for all purchased reagents follow: Sigma‐Aldrich: β‐alanine (146064), dimethyl 2‐oxoglutarate (349631), fumaric acid (F‐8509), α‐ketoglutarate (disodium salt) (K3752), lactic acid (L1875), 2,4‐pyridinedicarboxylic acid (2,4‐PDA) (04473), sodium 2‐oxobutyrate (K0875), sodium 3‐methyl‐2‐oxobutyrate (198994), sodium (±)‐3‐methyl‐2‐oxovalerate (K7125), sodium 4‐methyl‐2‐oxovalerate (K0629), sodium pyruvate (P2256), succinic acid (S3674), sodium azide (S8032), and glutaric acid (G3407). Fisher Scientific: carbonyl cyanide 4‐(trifluoromethoxy) phenylhydrazone (FCCP, #50‐810‐552), 2,4‐PDA (AC13186), and cobalt (II) chloride (AC21413). Mouse monoclonal antibodies targeting c‐myc (9E10) and tubulin (E7) were obtained from Developmental Studies Hybridoma Bank (Iowa City, IA, USA). HRP‐labeled anti‐mouse (NA9310) and anti‐rabbit (NA9340) secondary antibodies were purchased from GE Life Sciences (Pittsburgh, PA, USA). Antibodies targeting epigenetic modifications of histone H3 were purchased from Active Motif (Carlsbad, CA)—H3K4me3 (39160), H3K9me3 (39162), H3K27me3 (39537), and H3K36me3 (61102).
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3

Molecular Profiling of Breast Cancer Cells

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MDA-MB-231 cells and MCF7 cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) with 10% fetal bovine serum (FBS). SYBR Green PCR master mix was purchased from ABI. Monoclonal antibodies against GPT2 were purchased from Proteintech. The antibody against ALDH were obtained from BD (Cat # :611195). Antibodies against CD24 PE (Cat #:12-0247), CD44 APC (Cat #:17-0441) were acquired from eBioscience. Antibodies against Shh (Cat # :2207), HIF1α (Cat # :3716), HIF1α hydroxylation (Cat # :3434), SUFU (Cat # :2520), PTCH1 (Cat # :2468), PTCH2 (Cat # :2470), Gli1 (Cat # :3538), Notch Receptor Interaction Antibody Sampler Kit (Cat # :8658), Notch Isoform Antibody Sampler Kit (Cat # :3640), β-cantenin (Cat # :8480), p-GSK3β(Cat # :5558s), GSK3β(Cat # :9315L), OCT4 (Cat # :2750), SOX2 (Cat # :2748S), NANOG (Cat # :4903) were purchased from Cell Signaling Technology. The antibody against β-actin came from Santa Cruz Biotechnology (Cat # :47778). The α-Ketoglutarate Colorimetric/Fluorometric Assay Kit were obstained from BioVision Technologies. The human breast tumor tissue microarrays were purchased from Shanghai Outdo Biotech Co., Ltd. Dimethyl succinate (Cat # V900547) and Dimethyl 2-oxoglutarate (Cat # 349631) were obtained from Sigma-Aldrich.
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4

Cultured Cell Lines for Cancer Research

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MDA-MB231 human mammary breast adenocarcinoma (ATCC), HeLa human cervix cancer adenocarcinoma (ATCC) and SiHa human cervix squamous cell carcinoma (ATCC) cells were routinely cultured in DMEM containing 4.5 g/l of glucose and 2 mM of Glutamax, and supplemented with 10% FBS. Assay medium was DMEM without glucose, L-glutamine, phenol red, sodium pyruvate and sodium bicarbonate (D5030, Sigma-Aldrich), reconstituted with 10 mM glucose, 10% FBS, and buffered at pH 7.4 with 3.7 g/L NaHCO3. Cells were grown at 37°C in a humidified 5% CO2 atmosphere. Where indicated, cells were treated with 2 mM of L-glutamine (Invitrogen), 2 mM of dimethyl-L-glutamate (Sigma), 2 mM of dimethyl-2-oxoglutarate (Sigma), 2 mM of D-glutamine (Sigma), 5 mM of reduced glutathione (Merck Millipore),10 nM of rapamycin (Sigma), 15 nM of AZD8055 (Selleckchem), 10-100 ng/ml of recombinant human EGF (PeproTech), 20 ng/ml of recombinant IL-6 (Sigma), 1-10µM of Stattic (Santa Cruz), 10 µM of BPTES or 0.25-1 IU/ml of asparaginase (Sigma). Reagents were dissolved either in DMSO or directly in DMEM according to manufacturer’s indications. When DMSO was used, an equal quantity was also added to control medium. All drugs and reagents were administrated to adherent cells in fresh assay medium.
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5

KDOAM-25 Synthesis and Derivates

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KDOAM-25 was kindly provided by Dr. Gian-Filippo Ruda and Prof. Paul Brennan (Target Discovery Institute, Structural Genomics Consortium, University of Oxford) [55] (link). Dimethyl-L-2HG and dimethyl-D-2HG were synthesized according to the described procedures [28] (link), [55] (link). Dimethyl-2-oxoglutarate, dimethylsuccinate and dimethylfumarate were purchased from Sigma-Aldrich, and octyl-L-2HG and octyl-D-2HG were purchased from Cambridge Bioscience.
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6

Potassium Phosphate Metabolic Assay

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Potassium dihydrogen phosphate, di-potassium hydrogen phosphate, EDTA, sodium hydroxide, aminooxyacetic acid (AOAA), l-tryptophan (l-Try), indole-3-pyruvic acid (IPA), phenylpyruvic acid (PPA), α-Keto-γ-methylthiobutyric acid sodium salt (KMB), se-methylselenocysteine hydrochloride (MSC), dimethyl-2-oxoglutarate (α-KG), l-phenyl alanine (l-Phe), 2-amino-2-methyl-1,3-propanediol, pyridoxal 5′-phosphate hydrate (PLP), 2,4-dinitrophenylhydrazine (DNPH), Phenylmethanesulfonyl fluoride (PMSF), RIPA buffer, protease inhibitor cocktail mix, and N-N-dimethyl formamide, pLKO.1 vector were purchased from Sigma-Aldrich (Darmstadt, Germany). BFF-122 was purchased from Axon Medchem (Groningen, Netherlands), NADPH was purchased from Acros Organics (New Jersey, NJ, USA). Plasmid pEGFP-N1 (Clontech, Takara Bio USA, Inc, Mountain View, CA, USA) was a generous gift from Dr. Gildert Lauter from the Department for Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden. HEPG2 cells and EMEM media were purchased from ATCC (Wesel, Germany).
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7

Small Molecule Inhibitors in Cell Culture

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Small molecule inhibitors were purchased from the following vendors: olaparib (CAT No. S1060, Selleckchem), N-Acetyl-L-cysteine (CAT No. A7250 Sigma-Aldrich), and Dimethyl 2-oxoglutarate (CAT No. 349631 Sigma-Aldrich). CB-839 was kindly provided by Calithera Biosciences, South San Francisco, CA. Drug dilution, use, and storage were performed following standard protocols. The final concentration of DMSO for in vitro cell biology experiments was maintained at levels ≤0.1%.
Cyst108, FT105, FT2821, and FT406 were primary cultures, and were grown in DMEM with 15% FBS. The other cell lines were cultured in RPMI 1640 with 10% FBS. For glutamine deprivation, cells were cultured in glutamine-free and pyruvate-free DMEM with 4.5 g/L glucose (Fisher Scientific, CAT No: SH30081) and 10% dialyzed FBS (Invitrogen, CAT No. 26400). For glucose deprivation, cells were cultured in glucose-free DMEM (Invitrogen, CAT No: A14430) with 10% FBS.
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8

Formulation and Characterization of Clofazimine Nanoparticles

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All reagents were analytical grade. 1,8-Octanediol, calcium pantothenate, citric acid, chloroform, clofazimine (CFZ), coumarin 6 (Cou-6), dimethyl 2-oxoglutarate, dimethyl sulfoxide (DMSO) anhydrous, diphenyl ether, Dulbecco’s Modified Eagle’s Medium - high glucose (DMEM), hexane, L-leucine, poly(vinyl alcohol) (PVA; Mw 31,000–50,000; 98–99% hydrolysed), phosphate buffered saline tablets, phenol red, phorbol 12-myristate 13-acetate (PMA), silicon oil, sodium phosphate dibasic, Tween 80 and tricaine were purchased from Sigma-Aldrich, Merck (UK). Dichloromethane, formaldehyde, hygromycin B, methanol, Middlebrook 7H9 with OADC, Remel Middlebrook 7H10 Agar (Dehydrated) and trifluoroacetic acid (TFA) were acquired from Thermo Fisher Scientific (UK). Dimethyl sulphoxide-[D₆] (99.8% D), fetal calf serum (FCS; Sera Plus, EU approved regions, special processed FBS, 0.2 μm sterile filtered) and macrophage colony stimulating factor (MCSF) were purchased from VWR (UK), PanBiotech (Germany) and Peprotech (UK), respectively.
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9

Comprehensive Compound Sourcing for Metabolic Research

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IOX1,
IOX2, ML324, KDMOAM25, succinate,
fumarate, 2OG, dimethylpyridine-2,4-dicarboxylate, dimethyl 2-oxoglutarate,
dimethyl succinate, dimethyl fumarate, and DMOG were purchased from
Sigma-Aldrich, while IOX3, IOX4, Roxadustat, Vadadustat, Panobinostat,
disodium 2S/2R-hydroxyglutarate, and FG0041 were
obtained from Cayman Chemical Company. 2,4-PDCA (Alfa Aesar), Daprodustat
(MedChemExpress), QC6352 (MedChemExpress), Molidustat (Selleck Chem),
JIB-04 (Tocris Bioscience), GSK-J1 (Tocris Bioscience), GSK-J4 (Tocris
Bioscience), SD70 (Xcess Biosciences), CPI455 (Axon Med Chem), 2′-deoxy-5-methylcytidine
(TCI Chemicals), 2′-deoxy-5-(hydroxymethyl)cytidine (TCI Chemicals),
and (R/S)-Octyl-α-hydroxyglutarate
(Cambridge Bioscience) were purchased from other commercial sources.
All purchased inhibitors were >95% pure as determined by the manufacturer.
Key compound purity was verified using analytical HPLC using a UV
detector (210 or 254 nm) or CAD detector (Figures S18–S28). NOG was synthesized as described in the materials
and methods and has a purity >95% as determined by HPLC. All buffer
components were from Sigma-Aldrich unless otherwise stated.
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10

Metabolic Modulators for Cell Line Screening

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Ponatinib, Bazedoxifene and Lopinavir were purchased from Selleck Chemicals (Houston, TX, USA). 2-Deoxy-D-glucose (2-DG), O-benzyl-L-Serine (BenSer), 6-diazo-5-oxo-norleucine (DON), bis-2-(5-phenylacetamido-1,2,4-thiadiazol-2-yl)ethyl sulfide (BPTES), Telaglenastat (CB-839), epigallocatechin gallate (EGCG), 2-allyl-1-hydroxy-9,10-anthraquinone (R162), L-buthionine-sulfoximine (BSO), L-glutamine, glutamic acid and dimethyl 2-oxoglutarate were all purchased from Sigma (Sigma-Aldrich, St. Louis, MO, USA). The caspase-3 fluorescence dye was from Sartorius (Sartorius AG, Göttingen, Germany). Human IL-11Rα and negative control siRNA were from Thermofisher Scientific (Scoresby, VIC, Australia).
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