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Metabolomics Platform

Hypoxia-Mediated Increases in L-2-hydroxyglutarate Coordinate the Metabolic Response to Reductive Stress.
Oldham WM, Clish CB, Yang Y, Loscalzo J. Hypoxia-Mediated Increases in L-2-hydroxyglutarate Coordinate the Metabolic Response to Reductive Stress. Cell Metab. 2015;22(2):291-303. doi:10.1016/j.cmet.2015.06.021.
Organization of the Mammalian Metabolome according to Organ Function, Lineage Specialization, and Longevity.
Ma S, Yim SHee, Lee S-G, et al. Organization of the Mammalian Metabolome according to Organ Function, Lineage Specialization, and Longevity. Cell Metab. 2015;22(2):332-43. doi:10.1016/j.cmet.2015.07.005.
A roadmap for interpreting (13)C metabolite labeling patterns from cells.
Buescher JM, Antoniewicz MR, Boros LG, et al. A roadmap for interpreting (13)C metabolite labeling patterns from cells. Curr Opin Biotechnol. 2015;34:189-201. doi:10.1016/j.copbio.2015.02.003.
Functional genomics identifies negative regulatory nodes controlling phagocyte oxidative burst.
Graham DB, Becker CE, Doan A, et al. Functional genomics identifies negative regulatory nodes controlling phagocyte oxidative burst. Nat Commun. 2015;6:7838. doi:10.1038/ncomms8838.
Cross-sectional examination of metabolites and metabolic phenotypes in uremia.
Kalim S, Clish CB, Deferio JJ, et al. Cross-sectional examination of metabolites and metabolic phenotypes in uremia. BMC Nephrol. 2015;16:98. doi:10.1186/s12882-015-0100-y.
Metabolic control of type 1 regulatory T cell differentiation by AHR and HIF1-α.
Mascanfroni ID, Takenaka MC, Yeste A, et al. Metabolic control of type 1 regulatory T cell differentiation by AHR and HIF1-α. Nat Med. 2015;21(6):638-46. doi:10.1038/nm.3868.
The cytoplasmic prolyl-tRNA synthetase of the malaria parasite is a dual-stage target of febrifugine and its analogs.
Herman JD, Pepper LR, Cortese JF, et al. The cytoplasmic prolyl-tRNA synthetase of the malaria parasite is a dual-stage target of febrifugine and its analogs. Sci Transl Med. 2015;7(288):288ra77. doi:10.1126/scitranslmed.aaa3575.
Distinct metabolomic signatures are associated with longevity in humans.
Cheng S, Larson MG, McCabe EL, et al. Distinct metabolomic signatures are associated with longevity in humans. Nat Commun. 2015;6:6791. doi:10.1038/ncomms7791.
Flavin-containing monooxygenase 3 as a potential player in diabetes-associated atherosclerosis.
Miao J, Ling AV, Manthena PV, et al. Flavin-containing monooxygenase 3 as a potential player in diabetes-associated atherosclerosis. Nat Commun. 2015;6:6498. doi:10.1038/ncomms7498.
Metabolomics of renal venous plasma from individuals with unilateral renal artery stenosis and essential hypertension.
Rhee EP, Clish CB, Pierce KA, Saad A, Lerman LO, Textor SC. Metabolomics of renal venous plasma from individuals with unilateral renal artery stenosis and essential hypertension. J Hypertens. 2015;33(4):836-42. doi:10.1097/HJH.0000000000000470.
The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes.
Kostic AD, Gevers D, Siljander H, et al. The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Cell Host Microbe. 2015;17(2):260-73. doi:10.1016/j.chom.2015.01.001.
Pyruvate kinase M2 regulates Hif-1α activity and IL-1β induction and is a critical determinant of the warburg effect in LPS-activated macrophages.
Palsson-McDermott EM, Curtis AM, Goel G, et al. Pyruvate kinase M2 regulates Hif-1α activity and IL-1β induction and is a critical determinant of the warburg effect in LPS-activated macrophages. Cell Metab. 2015;21(1):65-80. doi:10.1016/j.cmet.2014.12.005.
Effects of sodium benzoate, a widely used food preservative, on glucose homeostasis and metabolic profiles in humans.
Lennerz BS, Vafai SB, Delaney NF, et al. Effects of sodium benzoate, a widely used food preservative, on glucose homeostasis and metabolic profiles in humans. Mol Genet Metab. 2015;114(1):73-9. doi:10.1016/j.ymgme.2014.11.010.
HdhQ111 Mice Exhibit Tissue Specific Metabolite Profiles that Include Striatal Lipid Accumulation.
Carroll JB, Deik A, Fossale E, et al. HdhQ111 Mice Exhibit Tissue Specific Metabolite Profiles that Include Striatal Lipid Accumulation. PLoS One. 2015;10(8):e0134465. doi:10.1371/journal.pone.0134465.
5-hydroxymethylcytosine is not present in appreciable quantities in Arabidopsis DNA.
Erdmann RM, Souza AL, Clish CB, Gehring M. 5-hydroxymethylcytosine is not present in appreciable quantities in Arabidopsis DNA. G3 (Bethesda). 2014;5(1):1-8. doi:10.1534/g3.114.014670.
Elevation of circulating branched-chain amino acids is an early event in human pancreatic adenocarcinoma development.
Mayers JR, Wu C, Clish CB, et al. Elevation of circulating branched-chain amino acids is an early event in human pancreatic adenocarcinoma development. Nat Med. 2014;20(10):1193-8. doi:10.1038/nm.3686.
Cell-state-specific metabolic dependency in hematopoiesis and leukemogenesis.
Wang Y-H, Israelsen WJ, Lee D, et al. Cell-state-specific metabolic dependency in hematopoiesis and leukemogenesis. Cell. 2014;158(6):1309-23. doi:10.1016/j.cell.2014.07.048.
Identification of small compound biomarkers of pituitary adenoma: a bilateral inferior petrosal sinus sampling study.
Oklu R, Deipolyi AR, Wicky S, et al. Identification of small compound biomarkers of pituitary adenoma: a bilateral inferior petrosal sinus sampling study. J Neurointerv Surg. 2014;6(7):541-6. doi:10.1136/neurintsurg-2013-010821.
Neuronal Tsc1/2 complex controls autophagy through AMPK-dependent regulation of ULK1.
Di Nardo A, Wertz MH, Kwiatkowski E, et al. Neuronal Tsc1/2 complex controls autophagy through AMPK-dependent regulation of ULK1. Hum Mol Genet. 2014;23(14):3865-74. doi:10.1093/hmg/ddu101.
Rictor/mTORC2 loss in the Myf5 lineage reprograms brown fat metabolism and protects mice against obesity and metabolic disease.
Hung C-M, Calejman CMartinez, Sanchez-Gurmaches J, et al. Rictor/mTORC2 loss in the Myf5 lineage reprograms brown fat metabolism and protects mice against obesity and metabolic disease. Cell Rep. 2014;8(1):256-71. doi:10.1016/j.celrep.2014.06.007.
Knockdown of malic enzyme 2 suppresses lung tumor growth, induces differentiation and impacts PI3K/AKT signaling.
Ren J-G, Seth P, Clish CB, et al. Knockdown of malic enzyme 2 suppresses lung tumor growth, induces differentiation and impacts PI3K/AKT signaling. Sci Rep. 2014;4:5414. doi:10.1038/srep05414.
Age- and diet-associated metabolome remodeling characterizes the aging process driven by damage accumulation.
Avanesov AS, Ma S, Pierce KA, et al. Age- and diet-associated metabolome remodeling characterizes the aging process driven by damage accumulation. eLife. 2014;3:e02077.
A systematic survey of lipids across mouse tissues.
Jain M, Ngoy S, Sheth SA, et al. A systematic survey of lipids across mouse tissues. Am J Physiol Endocrinol Metab. 2014;306(8):E854-68. doi:10.1152/ajpendo.00371.2013.
Inhibition of ATPIF1 ameliorates severe mitochondrial respiratory chain dysfunction in mammalian cells.
Chen WW, Birsoy K, Mihaylova MM, et al. Inhibition of ATPIF1 ameliorates severe mitochondrial respiratory chain dysfunction in mammalian cells. Cell Rep. 2014;7(1):27-34. doi:10.1016/j.celrep.2014.02.046.
Metabolic determinants of cancer cell sensitivity to glucose limitation and biguanides.
Birsoy K, Possemato R, Lorbeer FK, et al. Metabolic determinants of cancer cell sensitivity to glucose limitation and biguanides. Nature. 2014;508(7494):108-12. doi:10.1038/nature13110.
Regulation of ferroptotic cancer cell death by GPX4.
Yang WSeok, SriRamaratnam R, Welsch ME, et al. Regulation of ferroptotic cancer cell death by GPX4. Cell. 2014;156(1-2):317-31. doi:10.1016/j.cell.2013.12.010.
β-Aminoisobutyric acid induces browning of white fat and hepatic β-oxidation and is inversely correlated with cardiometabolic risk factors.
Roberts LD, Boström P, O'Sullivan JF, et al. β-Aminoisobutyric acid induces browning of white fat and hepatic β-oxidation and is inversely correlated with cardiometabolic risk factors. Cell Metab. 2014;19(1):96-108. doi:10.1016/j.cmet.2013.12.003.
A genomic and evolutionary approach reveals non-genetic drug resistance in malaria.
Herman JD, Rice DP, Ribacke U, et al. A genomic and evolutionary approach reveals non-genetic drug resistance in malaria. Genome Biol. 2014;15(11):511. doi:10.1186/PREACCEPT-1067113631444973.
Meclizine inhibits mitochondrial respiration through direct targeting of cytosolic phosphoethanolamine metabolism.
Gohil VM, Zhu L, Baker CD, et al. Meclizine inhibits mitochondrial respiration through direct targeting of cytosolic phosphoethanolamine metabolism. J Biol Chem. 2013;288(49):35387-95. doi:10.1074/jbc.M113.489237.
A plasma long-chain acylcarnitine predicts cardiovascular mortality in incident dialysis patients.
Kalim S, Clish CB, Wenger J, et al. A plasma long-chain acylcarnitine predicts cardiovascular mortality in incident dialysis patients. J Am Heart Assoc. 2013;2(6):e000542. doi:10.1161/JAHA.113.000542.
Branched chain and aromatic amino acids change acutely following two medical therapies for type 2 diabetes mellitus.
Walford GA, Davis J, A Warner S, et al. Branched chain and aromatic amino acids change acutely following two medical therapies for type 2 diabetes mellitus. Metabolism. 2013;62(12):1772-8. doi:10.1016/j.metabol.2013.07.003.
Reproducibility of metabolomic profiles among men and women in 2 large cohort studies.
Townsend MK, Clish CB, Kraft P, et al. Reproducibility of metabolomic profiles among men and women in 2 large cohort studies. Clin Chem. 2013;59(11):1657-67. doi:10.1373/clinchem.2012.199133.
PKM2 isoform-specific deletion reveals a differential requirement for pyruvate kinase in tumor cells.
Israelsen WJ, Dayton TL, Davidson SM, et al. PKM2 isoform-specific deletion reveals a differential requirement for pyruvate kinase in tumor cells. Cell. 2013;155(2):397-409. doi:10.1016/j.cell.2013.09.025.
2-Aminoadipic acid is a biomarker for diabetes risk.
Wang TJ, Ngo D, Psychogios N, et al. 2-Aminoadipic acid is a biomarker for diabetes risk. J Clin Invest. 2013;123(10):4309-17. doi:10.1172/JCI64801.
Metabolite profiles during oral glucose challenge.
Ho JE, Larson MG, Vasan RS, et al. Metabolite profiles during oral glucose challenge. Diabetes. 2013;62(8):2689-98. doi:10.2337/db12-0754.
A genome-wide association study of the human metabolome in a community-based cohort.
Rhee EP, Ho JE, Chen M-H, et al. A genome-wide association study of the human metabolome in a community-based cohort. Cell Metab. 2013;18(1):130-43. doi:10.1016/j.cmet.2013.06.013.
A combined epidemiologic and metabolomic approach improves CKD prediction.
Rhee EP, Clish CB, Ghorbani A, et al. A combined epidemiologic and metabolomic approach improves CKD prediction. J Am Soc Nephrol. 2013;24(8):1330-8. doi:10.1681/ASN.2012101006.
Letm1, the mitochondrial Ca2+/H+ antiporter, is essential for normal glucose metabolism and alters brain function in Wolf-Hirschhorn syndrome.
Jiang D, Zhao L, Clish CB, Clapham DE. Letm1, the mitochondrial Ca2+/H+ antiporter, is essential for normal glucose metabolism and alters brain function in Wolf-Hirschhorn syndrome. Proc Natl Acad Sci U S A. 2013;110(24):E2249-54. doi:10.1073/pnas.1308558110.
SIRT4 has tumor-suppressive activity and regulates the cellular metabolic response to DNA damage by inhibiting mitochondrial glutamine metabolism.
Jeong SMin, Xiao C, Finley LWS, et al. SIRT4 has tumor-suppressive activity and regulates the cellular metabolic response to DNA damage by inhibiting mitochondrial glutamine metabolism. Cancer Cell. 2013;23(4):450-63. doi:10.1016/j.ccr.2013.02.024.
PGC1α expression defines a subset of human melanoma tumors with increased mitochondrial capacity and resistance to oxidative stress.
Vazquez F, Lim J-H, Chim H, et al. PGC1α expression defines a subset of human melanoma tumors with increased mitochondrial capacity and resistance to oxidative stress. Cancer Cell. 2013;23(3):287-301. doi:10.1016/j.ccr.2012.11.020.
Circulating branched-chain amino acid concentrations are associated with obesity and future insulin resistance in children and adolescents.
McCormack SE, Shaham O, McCarthy MA, et al. Circulating branched-chain amino acid concentrations are associated with obesity and future insulin resistance in children and adolescents. Pediatr Obes. 2013;8(1):52-61. doi:10.1111/j.2047-6310.2012.00087.x.
MCT1-mediated transport of a toxic molecule is an effective strategy for targeting glycolytic tumors.
Birsoy K, Wang T, Possemato R, et al. MCT1-mediated transport of a toxic molecule is an effective strategy for targeting glycolytic tumors. Nat Genet. 2013;45(1):104-8. doi:10.1038/ng.2471.
The deacetylase Sirt6 activates the acetyltransferase GCN5 and suppresses hepatic gluconeogenesis.
Dominy JE, Lee Y, Jedrychowski MP, et al. The deacetylase Sirt6 activates the acetyltransferase GCN5 and suppresses hepatic gluconeogenesis. Mol Cell. 2012;48(6):900-13. doi:10.1016/j.molcel.2012.09.030.
mTOR complex 1 plays critical roles in hematopoiesis and Pten-loss-evoked leukemogenesis.
Kalaitzidis D, Sykes SM, Wang Z, et al. mTOR complex 1 plays critical roles in hematopoiesis and Pten-loss-evoked leukemogenesis. Cell Stem Cell. 2012;11(3):429-39. doi:10.1016/j.stem.2012.06.009.
Metabolite profiling identifies a key role for glycine in rapid cancer cell proliferation.
Jain M, Nilsson R, Sharma S, et al. Metabolite profiling identifies a key role for glycine in rapid cancer cell proliferation. Science. 2012;336(6084):1040-4. doi:10.1126/science.1218595.
Metabolite profiling identifies pathways associated with metabolic risk in humans.
Cheng S, Rhee EP, Larson MG, et al. Metabolite profiling identifies pathways associated with metabolic risk in humans. Circulation. 2012;125(18):2222-31. doi:10.1161/CIRCULATIONAHA.111.067827.
Targeted metabolomics.
Roberts LD, Souza AL, Gerszten RE, Clish CB. Targeted metabolomics. Curr Protoc Mol Biol. 2012;Chapter 30:Unit 30.2.1-24. doi:10.1002/0471142727.mb3002s98.
Metabolic consequences of mitochondrial coenzyme A deficiency in patients with PANK2 mutations.
Leoni V, Strittmatter L, Zorzi G, et al. Metabolic consequences of mitochondrial coenzyme A deficiency in patients with PANK2 mutations. Mol Genet Metab. 2012;105(3):463-71. doi:10.1016/j.ymgme.2011.12.005.
Skeletal muscle transcriptional coactivator PGC-1α mediates mitochondrial, but not metabolic, changes during calorie restriction.
Finley LWS, Lee J, Souza A, et al. Skeletal muscle transcriptional coactivator PGC-1α mediates mitochondrial, but not metabolic, changes during calorie restriction. Proc Natl Acad Sci U S A. 2012;109(8):2931-6. doi:10.1073/pnas.1115813109.
Programming human pluripotent stem cells into white and brown adipocytes.
Ahfeldt T, Schinzel RT, Lee Y-K, et al. Programming human pluripotent stem cells into white and brown adipocytes. Nat Cell Biol. 2012;14(2):209-19. doi:10.1038/ncb2411.
Identification and validation of tetracyclic benzothiazepines as Plasmodium falciparum cytochrome bc1 inhibitors.
Dong CK, Urgaonkar S, Cortese JF, et al. Identification and validation of tetracyclic benzothiazepines as Plasmodium falciparum cytochrome bc1 inhibitors. Chem Biol. 2011;18(12):1602-10. doi:10.1016/j.chembiol.2011.09.016.
A haploid genetic screen identifies the major facilitator domain containing 2A (MFSD2A) transporter as a key mediator in the response to tunicamycin.
Reiling JH, Clish CB, Carette JE, Varadarajan M, Brummelkamp TR, Sabatini DM. A haploid genetic screen identifies the major facilitator domain containing 2A (MFSD2A) transporter as a key mediator in the response to tunicamycin. Proc Natl Acad Sci U S A. 2011;108(29):11756-65. doi:10.1073/pnas.1018098108.
A hypoxia-induced positive feedback loop promotes hypoxia-inducible factor 1alpha stability through miR-210 suppression of glycerol-3-phosphate dehydrogenase 1-like.
Kelly TJ, Souza AL, Clish CB, Puigserver P. A hypoxia-induced positive feedback loop promotes hypoxia-inducible factor 1alpha stability through miR-210 suppression of glycerol-3-phosphate dehydrogenase 1-like. Mol Cell Biol. 2011;31(13):2696-706. doi:10.1128/MCB.01242-10.
Lipid profiling identifies a triacylglycerol signature of insulin resistance and improves diabetes prediction in humans.
Rhee EP, Cheng S, Larson MG, et al. Lipid profiling identifies a triacylglycerol signature of insulin resistance and improves diabetes prediction in humans. J Clin Invest. 2011;121(4):1402-11. doi:10.1172/JCI44442.
Metabolite profiles and the risk of developing diabetes.
Wang TJ, Larson MG, Vasan RS, et al. Metabolite profiles and the risk of developing diabetes. Nat Med. 2011;17(4):448-53. doi:10.1038/nm.2307.
SIRT3 opposes reprogramming of cancer cell metabolism through HIF1α destabilization.
Finley LWS, Carracedo A, Lee J, et al. SIRT3 opposes reprogramming of cancer cell metabolism through HIF1α destabilization. Cancer Cell. 2011;19(3):416-28. doi:10.1016/j.ccr.2011.02.014.
Induction of erythroid differentiation in human erythroleukemia cells by depletion of malic enzyme 2.
Ren J-G, Seth P, Everett P, Clish CB, Sukhatme VP. Induction of erythroid differentiation in human erythroleukemia cells by depletion of malic enzyme 2. PLoS One. 2010;5(9). doi:10.1371/journal.pone.0012520.
Activation of a metabolic gene regulatory network downstream of mTOR complex 1.
Düvel K, Yecies JL, Menon S, et al. Activation of a metabolic gene regulatory network downstream of mTOR complex 1. Mol Cell. 2010;39(2):171-83. doi:10.1016/j.molcel.2010.06.022.
Metabolite profiling identifies markers of uremia.
Rhee EP, Souza A, Farrell L, et al. Metabolite profiling identifies markers of uremia. J Am Soc Nephrol. 2010;21(6):1041-1051. doi:10.1681/ASN.2009111132.
Metabolic signatures of exercise in human plasma.
Lewis GD, Farrell L, Wood MJ, et al. Metabolic signatures of exercise in human plasma. Sci Transl Med. 2010;2(33):33ra37. doi:10.1126/scitranslmed.3001006.
Nutrient-sensitized screening for drugs that shift energy metabolism from mitochondrial respiration to glycolysis.
Gohil VM, Sheth SA, Nilsson R, et al. Nutrient-sensitized screening for drugs that shift energy metabolism from mitochondrial respiration to glycolysis. Nat Biotechnol. 2010;28(3):249-55. doi:10.1038/nbt.1606.
A plasma signature of human mitochondrial disease revealed through metabolic profiling of spent media from cultured muscle cells.
Shaham O, Slate NG, Goldberger O, et al. A plasma signature of human mitochondrial disease revealed through metabolic profiling of spent media from cultured muscle cells. Proc Natl Acad Sci U S A. 2010;107(4):1571-5. doi:10.1073/pnas.0906039107.
The histone deacetylase Sirt6 regulates glucose homeostasis via Hif1alpha.
Zhong L, D'Urso A, Toiber D, et al. The histone deacetylase Sirt6 regulates glucose homeostasis via Hif1alpha. Cell. 2010;140(2):280-93. doi:10.1016/j.cell.2009.12.041.