#METABOLOMICS WORKBENCH Sethjparker_20210526_151006 DATATRACK_ID:2657 STUDY_ID:ST001860 ANALYSIS_ID:AN003015 PROJECT_ID:PR001173 VERSION 1 CREATED_ON July 16, 2021, 12:39 pm #PROJECT PR:PROJECT_TITLE Spontaneous hydrolysis and spurious metabolic properties of α-ketoglutarate PR:PROJECT_TITLE esters PR:PROJECT_TYPE Manuscript PR:PROJECT_SUMMARY α-ketoglutarate (KG), also referred to as 2-oxoglutarate, is a key intermediate PR:PROJECT_SUMMARY of cellular metabolism with pleiotropic functions. Cell-permeable esterified PR:PROJECT_SUMMARY analogs are widely used to study the role of KG in governing bioenergetic and PR:PROJECT_SUMMARY amino acid metabolism and DNA, RNA, and protein hydroxylation reactions, as PR:PROJECT_SUMMARY cellular membranes are thought to be impermeable to KG. Here we show that PR:PROJECT_SUMMARY esterified KG analogs rapidly hydrolyze in aqueous media, yielding KG that, in PR:PROJECT_SUMMARY contrast to prevailing assumptions, can be imported by many cell lines. PR:PROJECT_SUMMARY Esterified KG analogs exhibit spurious KG-independent effects on cellular PR:PROJECT_SUMMARY metabolism, including extracellular acidification, arising from rapid hydrolysis PR:PROJECT_SUMMARY and de-protonation of α-ketoesters, and significant analog-specific inhibitory PR:PROJECT_SUMMARY effects on glycolysis or mitochondrial respiration. In many cell lines, imported PR:PROJECT_SUMMARY KG metabolizes to succinate in the cytosol, and we observe minimal KG PR:PROJECT_SUMMARY utilization for mitochondrial metabolism in normal culture conditions. These PR:PROJECT_SUMMARY findings demonstrate that nuclear and cytosolic KG-dependent reactions may PR:PROJECT_SUMMARY derive KG from functionally distinct subcellular pools and sources. PR:INSTITUTE University of British Columbia PR:DEPARTMENT Biochemistry & Molecular Biology PR:LAST_NAME Parker PR:FIRST_NAME Seth PR:ADDRESS 950 W 28th Ave, Room 2099, Vancouver, British Columbia, Canada V6H 0B3 PR:EMAIL seth.parker@bcchr.ca PR:PHONE 6048753121 #STUDY ST:STUDY_TITLE Spontaneous hydrolysis and spurious metabolic properties of α-ketoglutarate ST:STUDY_TITLE esters ST:STUDY_SUMMARY 8988T cells treated with methyl acetate or 1 mM of alpha-ketoglutarate disodium ST:STUDY_SUMMARY salt or 1 mM of dimethyl-alpha-ketoglutarate for 3 hours prior to rapid ST:STUDY_SUMMARY quenching of metabolism and extraction of metabolites in 80% methanol (-80°C) ST:STUDY_SUMMARY containing internal QC standards. ST:INSTITUTE University of British Columbia ST:LAST_NAME Parker ST:FIRST_NAME Seth ST:ADDRESS 950 W 28th Ave, 2099, Vancouver, British Columbia, Canada V6H 0B3 ST:EMAIL seth.parker@bcchr.ca ST:NUM_GROUPS 3 ST:TOTAL_SUBJECTS 9 ST:NUM_MALES n/a ST:NUM_FEMALES n/a ST:STUDY_TYPE Manuscript ST:PHONE 6048753121 #SUBJECT SU:SUBJECT_TYPE Cultured cells SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 SU:CELL_BIOSOURCE_OR_SUPPLIER DSMZ SU:CELL_STRAIN_DETAILS 8988T SU:SUBJECT_COMMENTS pancreatic ductal adenocarcinoma SU:CELL_COUNTS 1-2x10^6 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS - veh_1 Treatment:vehicle RAW_FILE_NAME=veh_1 SUBJECT_SAMPLE_FACTORS - veh_2 Treatment:vehicle RAW_FILE_NAME=veh_2 SUBJECT_SAMPLE_FACTORS - veh_3 Treatment:vehicle RAW_FILE_NAME=veh_3 SUBJECT_SAMPLE_FACTORS - KG_1 Treatment:KG (1 mM) RAW_FILE_NAME=KG_1 SUBJECT_SAMPLE_FACTORS - KG_2 Treatment:KG (1 mM) RAW_FILE_NAME=KG_2 SUBJECT_SAMPLE_FACTORS - KG_3 Treatment:KG (1 mM) RAW_FILE_NAME=KG_3 SUBJECT_SAMPLE_FACTORS - DMKG_1 Treatment:DMKG (1 mM) RAW_FILE_NAME=DMKG_1 SUBJECT_SAMPLE_FACTORS - DMKG_2 Treatment:DMKG (1 mM) RAW_FILE_NAME=DMKG_2 SUBJECT_SAMPLE_FACTORS - DMKG_3 Treatment:DMKG (1 mM) RAW_FILE_NAME=DMKG_3 #COLLECTION CO:COLLECTION_SUMMARY Metabolites were initially extracted from samples by quickly aspirating the cell CO:COLLECTION_SUMMARY culture media and adding 1 mL of extraction buffer, consisting of 80% methanol CO:COLLECTION_SUMMARY (Fisher Scientific) and 500 nM metabolomics amino acid mix standard (Cambridge CO:COLLECTION_SUMMARY Isotope Laboratories). To effectively scale all harvested samples to equivalent CO:COLLECTION_SUMMARY volumes of extraction buffer, samples were fully dried down by Speedvac (Thermo CO:COLLECTION_SUMMARY Fisher, Waltham, MA) and reconstituted volumetrically by mixing the entire dried CO:COLLECTION_SUMMARY cell pellet sample with 1 mL of 80% methanol without QC standards in 2.0 mL CO:COLLECTION_SUMMARY screw cap vials containing ~100 µL of disruption beads (Research Products CO:COLLECTION_SUMMARY International, Mount Prospect, IL). Samples were scaled to a ratio of 1e6 cells CO:COLLECTION_SUMMARY to 1 mL of extraction solvent with all steps being carried out in a cold room. CO:COLLECTION_SUMMARY Each was homogenized for 10 cycles on a bead blaster homogenizer (Benchmark CO:COLLECTION_SUMMARY Scientific, Edison, NJ). Cycling consisted of a 30 sec homogenization time at 6 CO:COLLECTION_SUMMARY m/s followed by a 30 sec pause. Samples were subsequently spun at 21,000 x g for CO:COLLECTION_SUMMARY 3 min at 4°C. A set volume of each (450 µL) was transferred to a 1.5 mL tube CO:COLLECTION_SUMMARY and dried down by Speedvac concentration. Samples were reconstituted in 50 µL CO:COLLECTION_SUMMARY of Optima LC/MS grade water (Fisher Scientific, Waltham, MA). Samples were CO:COLLECTION_SUMMARY sonicated for 2 mins, then centrifuged at 21,000 x g for 3 min at 4°C. Twenty CO:COLLECTION_SUMMARY microliters were transferred to LC vials containing glass inserts for analysis. CO:COLLECTION_SUMMARY The remaining sample was placed in -80°C for long term storage. CO:SAMPLE_TYPE Cultured cells CO:STORAGE_CONDITIONS -80℃ #TREATMENT TR:TREATMENT_SUMMARY 8988T cells were treated with methyl acetate, which is used as a vehicle, 1 mM TR:TREATMENT_SUMMARY of alpha-ketoglutarate disodium salt, or 1 mM of dimethyl-alpha-ketoglutarate TR:TREATMENT_SUMMARY (prepared in methyl acetate) for 3 hours in DMEM supplemented with 10% dialyzed TR:TREATMENT_SUMMARY fetal bovine serum and 5% penstrep #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Dried samples were reconstituted in 50 µL of Optima LC/MS grade water (Fisher SP:SAMPLEPREP_SUMMARY Scientific, Waltham, MA). Samples were sonicated for 2 mins, then centrifuged at SP:SAMPLEPREP_SUMMARY 21,000 x g for 3 min at 4°C. Twenty microliters were transferred to LC vials SP:SAMPLEPREP_SUMMARY containing glass inserts for analysis. The remaining sample was placed in -80°C SP:SAMPLEPREP_SUMMARY for long term storage. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY Samples were subjected to an LC-MS analysis to detect and quantify known peaks. CH:CHROMATOGRAPHY_SUMMARY A metabolite extraction was carried out on each sample by quickly aspirating CH:CHROMATOGRAPHY_SUMMARY experimental media and adding 1 mL of 80% methanol containing internal QC CH:CHROMATOGRAPHY_SUMMARY standards. The LC column was a MilliporeTM ZIC-pHILIC (2.1 x150 mm, 5 μm) CH:CHROMATOGRAPHY_SUMMARY coupled to a Dionex Ultimate 3000TM system and the column oven temperature was CH:CHROMATOGRAPHY_SUMMARY set to 25oC for the gradient elution. A flow rate of 100 μL/min was used with CH:CHROMATOGRAPHY_SUMMARY the following buffers; A) 10 mM ammonium carbonate in water, pH 9.0, and B) neat CH:CHROMATOGRAPHY_SUMMARY acetonitrile. The gradient profile was as follows; 80-20%B (0-30 min), 20-80%B CH:CHROMATOGRAPHY_SUMMARY (30-31 min), 80-80%B (31-42 min). Injection volume was set to 2 μL for all CH:CHROMATOGRAPHY_SUMMARY analyses (42 min total run time per injection). CH:CHROMATOGRAPHY_TYPE HILIC CH:INSTRUMENT_NAME Thermo Dionex Ultimate 3000 CH:COLUMN_NAME SeQuant ZIC- pHILIC (150 x 2.1mm, 5um) CH:FLOW_RATE 100 uL/min CH:COLUMN_TEMPERATURE 25 CH:SOLVENT_A 10 mM ammonium carbonate in water, pH 9.0 CH:SOLVENT_B acetonitrile #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo Q Exactive HF hybrid Orbitrap MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:ION_MODE NEGATIVE MS:MS_COMMENTS MS analyses were carried out by coupling the LC system to a Thermo Q Exactive MS:MS_COMMENTS HFTM mass spectrometer operating in heated electrospray ionization mode (HESI). MS:MS_COMMENTS Method duration was 30 min with a polarity switching data-dependent Top 5 method MS:MS_COMMENTS for both positive and negative modes. Spray voltage for both positive and MS:MS_COMMENTS negative modes was 3.5 kV and capillary temperature was set to 320oC with a MS:MS_COMMENTS sheath gas rate of 35, aux gas of 10, and max spray current of 100 μA. The full MS:MS_COMMENTS MS scan for both polarities utilized 120,000 resolution with an AGC target of MS:MS_COMMENTS 3e6 and a maximum IT of 100 ms, and the scan range was from 67-1000 m/z. Tandem MS:MS_COMMENTS MS spectra for both positive and negative mode used a resolution of 15,000, AGC MS:MS_COMMENTS target of 1e5, maximum IT of 50 ms, isolation window of 0.4 m/z, isolation MS:MS_COMMENTS offset of 0.1 m/z, fixed first mass of 50 m/z, and 3-way multiplexed normalized MS:MS_COMMENTS collision energies (nCE) of 10, 30, 80. The minimum AGC target was 1e4 with an MS:MS_COMMENTS intensity threshold of 2e5. All data were acquired in profile mode. The MS:MS_COMMENTS resulting ThermoTM RAW files were read with ThermoFisher CommonCore MS:MS_COMMENTS RawFileReader, and an in-house python script (Skeleton) was used for peak MS:MS_COMMENTS detection and quantification of all internal standards and sample peaks based on MS:MS_COMMENTS a previously established library of metabolite retention times and accurate MS:MS_COMMENTS masses adapted from the Whitehead Institute, and verified with authentic MS:MS_COMMENTS standards and/or high resolution MS/MS spectral manually curated against the MS:MS_COMMENTS NIST14MS/MS and METLIN (2017) tandem mass spectral libraries. MS:MS_RESULTS_FILE ST001860_AN003015_Results.txt UNITS:ion counts Has m/z:Yes Has RT:Yes RT units:Minutes #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS ion counts MS_METABOLITE_DATA_START Samples veh_1 veh_2 veh_3 KG_1 KG_2 KG_3 DMKG_1 DMKG_2 DMKG_3 Factors Treatment:vehicle Treatment:vehicle Treatment:vehicle Treatment:KG (1 mM) Treatment:KG (1 mM) Treatment:KG (1 mM) Treatment:DMKG (1 mM) Treatment:DMKG (1 mM) Treatment:DMKG (1 mM) 2,3-Diphosphoglyceric acid 17275 17275 17275 17275 17275 17275 17275 17275 17275 3-Hydroxybutyric acid 5062673.5 5062673.5 5062673.5 5062673.5 5062673.5 5062673.5 5062673.5 5062673.5 5062673.5 3-Phosphoglyceric acid 15357 15357 15357 16519 15357 40346 16609 15357 15357 4,5-Dihydroorotic acid 14092.5 14092.5 14092.5 14092.5 14092.5 14092.5 14092.5 14092.5 14092.5 5-Phosphoribosylamine 10000 10000 10000 10000 10000 10000 10000 10000 10000 6-Phosphogluconic acid 13584 13584 13584 13584 13584 13584 13584 13584 13584 Acetoacetic acid 118683.5 118683.5 118683.5 145633 119737 135244 118683.5 118683.5 118683.5 Adenosine diphosphate ribose 10784.5 14258 31551 24888 10784.5 28702 21753 10784.5 14325 Adenosine triphosphate 37495 39765 37495 53000 37495 51688 63410 37495 46029 Adenylsuccinic acid 10000 10000 10000 10000 10000 10000 10000 10000 10000 ADP 65959 65959 65959 72885 65959 91215 66212 65959 65959 Allantoin 21376 28825 23860 21673 23964 23974 35266 37202 26125 Aminoadipic acid 742392 1060873 1429260 1342694 1153650 1840811 1466279 1212977 1407958 Argininosuccinic acid 11388.5 11388.5 11388.5 11388.5 11388.5 18863 56743 33117 48657 Carbamoyl phosphate 15266.5 15266.5 15266.5 15266.5 15266.5 15266.5 15266.5 15266.5 15266.5 cis-Aconitic acid 2621500 3199978 3386901 4383227 3075470 4408516 6663232 4442668 6280930 Citric acid 321442 321442 321442 709935 321442 1074635 1104618 409391 1022127 Cyclic AMP 10836 10000 16708 15508 12625 18128 17182 14512 13517 Cytidine triphosphate 11834.5 11834.5 11834.5 11834.5 11834.5 11834.5 11834.5 11834.5 11834.5 D-2-Hydroxyglutaric acid 648087 886967 1105866 1302175 1041870 1588352 4405415 2849337 3546333 D-Glucose 13571387 15191066 19322880 17496420 16404799 20517378 19872596 16799792 18797498 D-Glyceraldehyde 3-phosphate 12416 12416 12416 12416 12416 12416 12416 12416 12416 Dihydroxyacetone phosphate 79909 151295 168670 226576 148612 271372 165205 90656 145496 D-Ribose 5-phosphate 31148 45577 40980 93005 69127 233703 51027 42972 38067 D-Sedoheptulose 7-phosphate 19148 20329 24697 30448 17479 39671 42906 27184 33467 dTDP 11114.5 11114.5 11114.5 11114.5 11114.5 11114.5 11114.5 11114.5 11114.5 Fructose 1,6-bisphosphate 10694 10694 10694 10694 10694 10694 10694 10694 10694 Fructose 6-phosphate 81197 124112 104465 178023 134126 264854 157833 81297 122811 Fumaric acid 1289357 1586562 1901462 2440619 1717420 4549376 9587739 7340844 8993491 Glucose 6-phosphate 293965 492685 452541 576833 441372 874516 571215 349059 734045 Glycerol 3-phosphate 660813 1028120 964804 1479194 1101668 2395761 1264464 724946 1163591 Guanosine diphosphate 13233.5 13233.5 13233.5 13233.5 13233.5 13233.5 13233.5 13233.5 13233.5 Guanosine triphosphate 10000 10000 10000 10000 10000 10000 10000 10000 10000 Homocysteine 10859 10859 10859 10859 10859 10859 10859 10859 10859 L-Aspartic acid 13356314 15692725 16806956 17417370 14968908 15250917 37506916 31578560 36945512 L-Cystine 340929 561551 825225 233902 143976 203740 162077 108146 152598 L-Lactic acid 20807254 26330298 31058576 33302772 27757884 39588552 28390524 19413534 21473202 L-Malic acid 22371478 26684776 30691290 43317656 29832890 90153440 136096544 105104104 130430264 L-Threonine 15203128 20347308 22476232 22888044 19128272 26705572 25337638 20540124 24229506 N-Acetylglutamine 54066 68500 85165 109445 74306 92703 130613 75512 89500 N-Acetylserine 8337286 11074774 12591269 13463451 11290738 15901635 14170906 10589457 13094227 NADH 70993 82283 95091 142511 104551 11948 126564 74169 60815 NADPH 10645.5 10645.5 10645.5 10645.5 10645.5 10645.5 10645.5 10645.5 10645.5 Nicotinic acid 48707 48707 48707 48707 48707 48707 48707 48707 48707 Orotic acid 45901 51473 117510 72909 69498 116169 78979 55203 97010 Oxoadipic acid 18393 18393 18393 18393 18393 18393 55752 50058 62886 Oxoglutaric acid 4720589 4720589 5059704 171147760 159098528 190401920 127153976 84432136 106727296 Palmitic acid 10526122 13231931 11742567 8990748 15755418 22264104 27769432 25574588 13953207 Phenol 2344528 2344528 2344528 2344528 2344528 2344528 2344528 2344528 2344528 Phosphocreatine 286097 497357 516780 625545 394151 750660 538857 287075 550842 Phosphoenolpyruvic acid 43643.5 56022 43643.5 105790 43643.5 333222 66464 43643.5 51931 Phosphoribosyl pyrophosphate 10000 10000 10000 10000 10000 10000 10000 10000 10000 Pyruvic acid 254417 177077 309257 537984 519382 3138472 455341 528608 649926 Ribose 1-phosphate 12713.5 12713.5 12713.5 12713.5 12713.5 12713.5 12713.5 12713.5 12829 Saccharopine 10616.5 10616.5 10616.5 10616.5 10616.5 10616.5 16793 10616.5 14219 S-Adenosylhomocysteine 10000 10000 10461 11415 10000 13629 16716 10000 10000 Succinic acid 1122269 1385384 1789396 10965860 8824452 10106919 8674890 5603230 7633037 Taurine 16144191 20892426 23251224 24990640 21162420 28297166 26740744 20496016 22861624 Thymidine 17531 17531 17531 17531 17531 17531 17531 17531 17531 Ureidopropionic acid 122232 155982 158605 202272 125042 408878 449946 375439 497404 Ureidosuccinic acid 62706 163360 177173 168165 84389 205076 155782 83280 126486 Uridine 321690 1810280 405614 749337 613062 2186774 3472786 948926 373451 Uridine 5'-monophosphate 92105 145958 167906 239069 93800 156500 54126.5 54126.5 158269 Uridine diphosphate glucose 293758 527328 569136 731860 524568 794808 661641 443422 575454 Uridine triphosphate 20178 20178 20178 20178 20178 22249 22934 20178 24245 Xanthine 61450 66346 92926 159477 66972 6953216 82868 54178 67823 Xanthosine 10643.5 10643.5 10643.5 10643.5 10643.5 34607 10643.5 10643.5 10643.5 Xanthylic acid 10000 10000 10000 10000 10000 10000 10000 10000 10000 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name 2,3-Diphosphoglyceric acid 3-Hydroxybutyric acid 3-Phosphoglyceric acid 4,5-Dihydroorotic acid 5-Phosphoribosylamine 6-Phosphogluconic acid Acetoacetic acid Adenosine diphosphate ribose Adenosine triphosphate Adenylsuccinic acid ADP Allantoin Aminoadipic acid Argininosuccinic acid Carbamoyl phosphate cis-Aconitic acid Citric acid Cyclic AMP Cytidine triphosphate D-2-Hydroxyglutaric acid D-Glucose D-Glyceraldehyde 3-phosphate Dihydroxyacetone phosphate D-Ribose 5-phosphate D-Sedoheptulose 7-phosphate dTDP Fructose 1,6-bisphosphate Fructose 6-phosphate Fumaric acid Glucose 6-phosphate Glycerol 3-phosphate Guanosine diphosphate Guanosine triphosphate Homocysteine L-Aspartic acid L-Cystine L-Lactic acid L-Malic acid L-Threonine N-Acetylglutamine N-Acetylserine NADH NADPH Nicotinic acid Orotic acid Oxoadipic acid Oxoglutaric acid Palmitic acid Phenol Phosphocreatine Phosphoenolpyruvic acid Phosphoribosyl pyrophosphate Pyruvic acid Ribose 1-phosphate Saccharopine S-Adenosylhomocysteine Succinic acid Taurine Thymidine Ureidopropionic acid Ureidosuccinic acid Uridine Uridine 5'-monophosphate Uridine diphosphate glucose Uridine triphosphate Xanthine Xanthosine Xanthylic acid METABOLITES_END #END