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22 protocols using sodium dichloroacetate

1

PDK Inhibition in Immune Response

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To inhibit PDK, cells were pretreated with 10mM sodium dichloroacetate (Sigma) 48h prior to LPS and IFN-γ stimulation, and the sodium dichloroacetate was kept in media throughout the stimulation time-course.
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2

Thiamine-deficient Cell Culture Reagents

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All cell culture reagents including gentamicin and trypsin/EDTA were obtained from Mediatech (Manassas, VA). Custom formulated thiamine-deficient RPMI 1640 was also prepared by Mediatech to allow for the controlled addition of thiamine. Cell culture treated flasks, plates, and dishes were obtained from Greiner Bio-one (Monroe, NC). Fetal bovine serum (FBS), crystal violet, thiamine hydrochloride, and sodium dichloroacetate (DCA) were purchased from Sigma Aldrich (St. Louis, MO).
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3

Modulators of Cellular Metabolism

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Vitamin K2 (V9378), α-D-Glucose (158968), 2-Deoxy-D-glucose (D8375), 3-Bromopyruvic acid (16490) and Sodium dichloroacetate (347795) were purchased from Sigma-Aldrich. Lificiguat (YC-1) (S7958) and Compound C (S7840) were purchased from Selleck. MK2206 dihydrochloride (HY-10358), LY294002 (HY-10108), Chloroquine (HY-17589), 3-Methyladenine (HY-19312) and Rapamycin (HY-10219) were purchased from MCE.
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4

Hepatoma Cell Culture Optimization

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PLC/PRF/5, human hepatoma cell line was obtained from the American Type Culture Collection (Rockville, MD). The cells were cultured in low glucose (5.5 mM) or high glucose (25 mM) Dulbecco's modified Eagle's medium (DMEM) containing 10% fetal bovine serum (FBS; Gibco) and antibiotic. Mito Tracker Green and Mito Tracker red CMXRos were obtained from Invitrogen. Sodium lactate and sodium dichloroacetate were obtained from Sigma-Aldrich. The antibodies obtained were: anti-CD133/1 (AC133)-PE and anti-CD133 (W6B3C1) pure (Miltenyi Biotec), anti-HNF4α (Santa Cruz Biotechnology), anti-HNF1α and anti-HNF3α (Millipore), anti-HNF1β (Genway), anti-PDK4 (ABGENT), and anti-β-actin (Sigma). Synthetic siRNAs against LDHA and PDK4, miR-122, U6 primers and mimic were obtained from Qiagen. Cells were transfected at a final concentration of 50 nM siRNA or 20 nM of miR-122 mimic using Oligofectamine reagent (Invitrogen) according to the manufacturer's instructions. The lentiviral particle expressing miR-122 and lentiviral negative control mimic were obtained from GenCopoiea.
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5

Cell Culture Reagents and Compounds

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Unless otherwise stated, we purchased all cell culture reagents from Life Technologies (Carlsbad, California, USA). We obtained drugs and compounds from the following sources: PD0325901 from SelleckChem (Houston, Texas, USA); D-glucose, 2-deoxy-D-glucose, rotenone, and sodium dichloroacetate from Sigma Aldrich (St. Louis, Missouri, USA); and oligomycin from Seahorse Biosciences (Agilent Technologies, Santa Clara, California, USA). We prepared a rotenone stock at 10mM in ethanol. We prepared all other compounds in formulations supplied or specified by manufacturers.
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6

Authenticated Cell Lines for Bladder Cancer

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Thoroughly tested and authenticated human high-grade BCa cell lines HTB-9, HT-1376, HTB-5 and HTB-4 were obtained from ATCC (Mannasas, VA). The UROtsa (benign) urothelial cell line was a gift from Dr. Brian Philips, University of Pittsburgh. Malignant cells were cultured in Eagle’s MEM (103700-021, Invitrogen, Grand Island, NY), and UROtsa cells were cultured in DMEM media, supplemented with 10% heat-inactivated fetal calf serum, 1 mM sodium pyruvate, 2 mM L-glutamine, 100 U/ml penicillin and 50 μg/ml streptomycin at 37°C in a 5% CO2 in air atmosphere. All cells were used below 20 passages to reduce cellular drift. Early aliquots from each cell line were tested for Mycoplasma using the MycoAlert test kit (Lonza, Basel, Switzerland) and found to be mycoplasma free. Dichloroacetate was acquired as the sodium salt (sodium Dichloroacetate) from Sigma-Aldrich. Cisplatin was acquired at United States Pharmacopeia grade via Sigma-Aldrich. All chemicals were acquired from Sigma-Aldrich unless otherwise noted.
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7

Metabolic Modulation: A Comprehensive Protocol

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Reagents used for experiments: 2-deoxy-d-glucose (D0051, TCI), l-phenylalanine (P0134, TCI), oligomycin A (75351, Sigma-Aldrich), rotenone (R8875, Sigma-Aldrich), FCCP (C2920, Sigma-Aldrich), sodium pyruvate (11360070, Gibco), sodium dichloroacetate (347795, Sigma-Aldrich), palmitic acid (P0500, Sigma-Aldrich), oleic acid (O1008, Sigma-Aldrich), l-glutamine (LS002-01, Welgene), CPI-613 (SML0404, Sigma-Aldrich), (+)-Etomoxir sodium salt hydrate (E1905, Sigma-Aldrich), BPTES (SML0601, Sigma-Aldrich), nicotinamide riboside chloride (SMB00907, Sigma-Aldrich),
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8

Cell Culture Reagent Sourcing

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Unless otherwise stated we purchased all cell culture reagents from Life Technologies (Carlsbad, CA, USA). We obtained drugs and compounds from the following sources: PD0325901 from SelleckChem (Houston, TX, USA); D-glucose, 2-deoxy-D-glucose, rotenone, and sodium dichloroacetate from Sigma Aldrich (St. Louis, MO, USA); and oligomycin from Seahorse Biosciences (Massachusetts, USA). We prepared a rotenone stock at 10 mM in ethanol. We prepared all other compounds in formulations supplied or specified by manufacturers.
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9

Comparative Cell Line Cultivation and Characterization

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The human HCC cell line HCCLM3 and mouse HCC cell line H22 were obtained from the China Center for Type Culture Collection, the mouse HCC cell line Hepa1–6 was obtained from Cell Bank of Type Culture Collection Chinese Academy of Sciences, authenticated by short tandem repeat (STR) analysis, and tested for mycoplasma contamination. HCCLM3 (abbreviated LM3) and Hepa1–6 cells were cultured in high glucose (4.5 g/L) Dulbecco’s modified Eagle’s medium (DMEM) and H22 cells were cultured in Roswell Park Memorial Institute 1640 Medium (RPMI 1640) supplemented with 10% foetal bovine serum, 2 mM l-glutamine, 100 units/mL penicillin, and 0.1 mg/mL streptomycin (all from Thermo Fisher Scientific, Gibco, Grand Island, NY, USA). All cells were maintained in a humidified incubator with an atmosphere containing 5% CO2 at 37 °C.
The following reagents were used: sodium dichloroacetate (#347795; Sigma-Aldrich, St. Louis, MO, USA), trypan blue (#ST798; Beyotime Biotechnology, Shanghai, China), and 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) (#M2128; Sigma-Aldrich).
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10

Rhabdomyosarcoma and myoblast cell culture with statins

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The human rhabdomyosarcoma cell line A-204 and the mouse myoblast C2C12 cell line were obtained from ATCC, and maintained in McCoy's 5A medium (Gibco) and Dulbecco's modified Eagle's medium (Gibco) respectively. C2C12 myoblasts were stimulated to differentiate into myotubes by switching to the medium with 2% horse serum. The human colon cancer HCT116 SCO2−/− cell line was a generous gift from Dr. Paul M. Hwang at the National Institutes of Health, and cultured in McCoy's 5A medium.
Lovastatin, fluvastatin sodium, simvastatin, rosuvastatin calcium, mevalonic acid sodium, sodium dichloroacetate, coenzyme Q10 (CoQ10) and oligomycin A were purchased from Sigma Aldrich. Pitavastatin and atorvastatin were purchased from Cayman Chemical. Nutlin-3 was purchased from Selleck Chemicals. The doses of statins in cell culture were consistent with previous studies in SAMS [18 (link)].
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