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46 protocols using oxaloacetate

1

Cell Culture and Metabolic Perturbations

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Jurkat, Jeko and Reh cell lines were maintained in RPMI1640 (Sigma, St. Louis, MO, USA) supplemented with 10% FCS, 100 units/mL penicillin and 100 μg/mL streptomycin. NK‐YS cell line was grown according to previous reports.3, 23 Cells were split to keep cell density from 3 × 105 to 1 × 106 cells/mL. To deplete Gln, Asn or glucose, cells were cultured in RPMI1640 completely lacking one of these nutrients (Sigma) supplemented with 10% dialyzed FCS. Logarithmically growing cells were treated with indicated doses of L‐ASNase (Kyowa Hakko Kirin), whose 1 U is equivalent to 1 E of Asparaginase medac (medac GmbH, Wedel, Germany). Dimethyl‐2‐oxoglutarate (DM‐OG), methylpyruvate, oxaloacetate, aminooxyacetate (AOA) and epigallocatechin gallate (EGCG) were purchased from Sigma.
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2

Mitochondrial Mass Quantification via Citrate Synthase

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Stored tissue was equilibrated with 1:40 volumes (w:v) ice-cold homogenization buffer (25 Tris-HCl pH 7.8, 1 EDTA, 2 MgCl2, 50 KCl, 0.5%v/v Triton X-100). Samples were then homogenized and citrate synthase (CS) activity determined using a plate reader (Molecular Devices Spectramax 340, Sunnyvale, USA) and 5 μl of sample supernatant was added to an assay media containing Tris-HCl (50 mM, pH 8.0), acetyl coenzyme A (0.1 mM), DTNB (0.2 mM). Reactions started by addition of 5 mM oxaloacetate (Sigma, St. Louis, USA), and followed the formation of mercaptide ions at 412 nm. CS activity (units per wet weight of tissue) was determined relative to CS standard (Sigma, St. Louis, USA) from porcine heart. CS data were used as a proxy of mitochondrial mass and used to normalize flux rates in order to estimate mitochondrial specific fluxes.
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3

Enzyme Purification and Characterization

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Purified enzymes were purchased from Sigma, including LDH from bovine heart (L2625), LDH from rabbit muscle (L2500), and MDH from porcine heart (M1567). Recombinant human enzymes were purchased from Abcam, including LDHA (ab93699), MDH1 (ab99244), MDH2 (ab99238), IDH1 (ab113858), and PHGDH (ab198455). Substrates, cofactors, and inhibitors were purchased from Sigma, including pyruvate, oxaloacetate, alpha-ketoglutarate, dimethyl-alpha-ketoglutarate, L-lactate, D-lactate, L-malate, D-malate, L-2-hydroxyglutarate, D-2-hydroxyglutarate, alpha-ketobutyrate, oxopentanoic acid, oxoadipic acid, ketohexanoic acid, phenylpyruvate, hydroxyphenylpyruvate, NADH, NADPH, and oxamate. FLAG-tagged wildtype and Q100R mutant LDHA constructs were cloned into the PCDNA3.1(+) vector (Addgene) by standard site-directed mutagenesis and verified by Sanger sequencing.
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4

Enzymatic Assays with Cofactors

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Materials including sulfopyruvate, oxaloacetate, α-ketoglutarate, NADPH, NADH, 3-(N-morpholino)propanesulfonic acid (Mops), 1,3-bis(tris(hydroxymethyl)methylamino)propane or Bis-Tris propane (BTP), tris(2-carboxyethyl)phosphine (TCEP), and dithiothreitol (DTT) were purchased from Sigma-Aldrich (USA). Other common chemicals were obtained from ThermoFisher Scientific (NZ).
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5

Metabolic Analysis of Cellular Compounds

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Cordycepin, streptozotocin (STZ), pentobarbital sodium, and TCA cycle standard samples (oxaloacetate, alpha-ketoglutarate, and citrate) were purchased from Sigma (St. Louis, USA).
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6

Citrate synthase activity assay

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Following treatments, cells were washed with PBS and lysed in 0.25% (v/v) Triton X-100 (Sigma-Aldrich, St. Louis, MO) in PBS supplemented with protease and phosphatase inhibitors. Debris was removed by centrifugation and citrate synthase (CS) activity was measured by following the oxidation of 5,5′-Dithiobis(2-nitrobenzoic acid) (Sigma-Aldrich, St. Louis, MO) in a spectrophotometer (absorbance at 412 nm) over time at 30°C in the presence of acetyl co-enzyme A (Sigma-Aldrich, St. Louis, MO) and oxaloacetate (Sigma-Aldrich, St. Louis, MO) (Clark and Land, 1974 (link)). Protein concentration was measured based on the bicinchoninic acid (BCA) method, using a Bicinchoninic Acid Kit (Sigma-Aldrich, St. Louis, MO) using bovine serum albumin (BSA) as a standard. The enzyme activity was expressed as nmol/min/mg protein.
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7

Comprehensive Biochemical Assays and Cell Culture Protocols

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Cell culture grade DMSO (Cat No D2650), Congo Red (Cat No C6277), Dulbecco’s phosphate buffered saline (DPBS, D8537), Evans Blue (Cat No E2129), β-nicotinamide adenine dinucleotide (NADH, Cat No N4505), oxaloacetate (Cat No O4126) and RPMI 1640 cell culture media (Cat No R8758) were purchased from Sigma-Aldrich. Fulvestrant (Cat No S1191) was purchased from Selleckchem. Lapatinib (HY-50898), nilotinib (Cat No HY-10159), sorafenib (Cat No HY-10201) and vemurafenib (Cat No HY-12057) were purchased from MedChem Express. 3′,3′′,5′,5′′-Tetraiodophenolphthalein (TIPT, Cat No sc-216639) was purchased from Santa Cruz Biotechnology. AmpC β-lactamase was purified from Escherichia coli as previously described.30 (link) Malate dehydrogenase (MDH, Cat No 442610) and CENTA (Cat No 219475) were purchased from EMD Millipore. Trypsin (Cat No T0303) and Suc-Ala-Ala-Pro-Arg-pNA (Cat No L1720) were purchased from Sigma-Aldrich and BACHEM respectively. Cell line MDA-MB-231 (Cat No HTB-26) was purchased from ATCC. Triton X-100 (Cat No 21568-2500) was purchased from Acros. Presto Blue cell viability reagent (Cat No A13262) was purchased from Invitrogen. 96-well plates (Cat No 655096) for DLS were purchased from Greiner Bio-One.
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8

Citrate Synthase Activity Assay

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Activity assays were performed using a citrate synthase activity assay kit (Sigma CS0720, St. Louis, MO, USA) per the manufacturer’s instructions. Briefly, skeletal muscles or primary myotube lysates were generated by glass pestle homogenization by hand in RIPA buffer. Protein concentrations were determined using a BCA Protein Assay (Pierce Thermo Fisher #23225, Waltham, MA, USA). Activity assays were performed in assay buffer containing (in mmol/L): 100 Tris, 1 EDTA, 1 EGTA, 10 DTNB (Sigma: D8130), and 30 Acetyl-CoA at pH 8.35. All samples were measured in duplicate and the average absorbance was used in final calculations of activity. Background absorbance was measured prior to addition of 10 mM oxaloacetate (Sigma: O4126) and final activity rates were corrected for those values.
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9

Apoptosis pathway inhibitors protocol

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ABT-263, A-1331852 and A-1210477 were from AbbVie (North Chicago, IL, USA),
ABT-199, epigallocatechin gallate (EGCG), CB-839, simvastatin, rapamycin and
torin-1 from Selleck Chemicals (Houston, TX, USA),
gamma-L-glutamyl-p-nitroanilide (GPNA) from Insight
Biotechnology (Wembley, Middlesex, UK), azaserine from Cambridge Bioscience
(Cambridge, UK), aminooxyacetate (AOA), sodium palmitate, dimethyl
α-ketoglutarate, oxaloacetate and citrate from Sigma-Aldrich
(Gillingham, UK), L-glutamine from Life Technologies (Paisley, UK) and
GSK2194069, SB204990, atorvastatin, pitavastatin and bafilomycin A1 from Tocris
(Abingdon, UK). Antibodies against PARP, BCL-2, MCL-1, BAX, BAK and GAPDH were
from Santa Cruz Biotechnology (Santa Cruz, CA, USA), caspase-3, caspase-9,
BCL-XL, BCL-w, BIM, PUMA, BAD, IDH2, ACL, ACO2, ATG5 and ATG7
from Cell Signaling Technology (MA, USA), BID from Prof. J. Borst (The
Netherlands Cancer Institute, Amsterdam, the Netherlands), NOXA from Millipore
(Watford, UK) and SLC1A5, GLS, GFAT, GLUD1, IDH3, FASN and HMGR from Abcam
(Cambridge, UK).
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10

Enzyme Inactivation Assay of CS

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The enzyme inactivation assay of CS was performed as described previously [31 (link), 32 (link)]. Briefly, CS (0.15 μM) was incubated at 43 °C in the absence or presence of IgG (1.2 μM), NudCL2 (0.6 μM) or Hsp90 (0.6 μM) in the inactivation buffer (40 mM HEPES-KOH, 0.1 mM EDTA, pH 7.5). Aliquots (100 μl) were taken at the indicated times and mixed with 650 μl of 100 mM Tris (pH 8.1), 50 μl of 3 mM acetyl-CoA (Sigma), 100 μl of 1 mM DTNB (Sigma), and 100 μl of 5 mM oxaloacetate (Sigma), and then incubated at 30 °C for 1 min to eliminate the false readings. To monitor CS activity, the readings were measured at 30 °C for 1 min with 20-s intervals at 412 nm by SpectraMax (Molecular Devices).
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