Anchoring Metabolomic Changes to Phenotype P20 Project

Publications

Zhu W, Gregory JC, Org E, Buffa JA, Gupta N, Wang Z, Li L, Fu X, Wu Y, Mehrabian M, Sartor RB, McIntyre TM, Silverstein RL, Tang WH, DiDonato JA, Brown JM, Lusis AJ, Hazen SL. Gut Microbial Metabolite TMAO Enhances Platelet Hyperreactivity and Thrombosis Risk. Cell. 2016 Mar 24;165(1):111-24. PMCID:PMC4862743

Seldin MM, Meng Y, Qi H, Zhu W, Wang Z, Hazen SL, Lusis AJ, Shih DM. Trimethylamine N-Oxide Promotes Vascular Inflammation Through Signaling of Mitogen-Activated Protein Kinase and Nuclear Factor-κB. J Am Heart Assoc. 2016 Feb 22;5(2). PMCID: PMC4802459

Hammadah M, Brennan ML, Wu Y, Hazen SL, Tang WH. Usefulness of Relative Hypochromia in Risk Stratification for Nonanemic Patients With Chronic Heart Failure. Am J Cardiol. 2016 Apr 15;117(8):1299-304. PMCID:PMC4811711

Kitai T, Kirsop J, Tang WH. Exploring the Microbiome in Heart Failure. Curr Heart Fail Rep. 2016 Apr;13(2):103-9. PMCID:PMC4791185

Hartiala JA, Tang WH, Wang Z, Crow AL, Stewart AF, Roberts R, McPherson R, Erdmann J, Willenborg C, Hazen SL, Allayee H. Genome-wide association study and targeted metabolomics identifies sex-specific association of CPS1 with coronary artery disease. Nat Commun. 2016 Jan 29;7:10558. PMCID:PMC4740183

Serban MC, Sahebkar A, Mikhailidis DP, Toth PP, Jones SR, Muntner P, Blaha MJ, Andrica F, Martin SS, Borza C, Lip GY, Ray KK, Rysz J, Hazen SL, Banach M. Impact of L-carnitine on plasma lipoprotein(a) concentrations: A systematic review and meta-analysis of randomized controlled trials. Sci Rep. 2016 Jan 12;6:19188. PMCID:PMC4709689 

Grodin JL, Verbrugge FH, Ellis SG, Mullens W, Testani JM, Tang WH. Importance of Abnormal Chloride Homeostasis in Stable Chronic Heart Failure. Circ Heart Fail. 2016 Jan;9(1):e002453. PMCID:PMC4702267

Organ CL, Otsuka H, Bhushan S, Wang Z, Bradley J, Trivedi R, Polhemus DJ, Tang WH, Wu Y, Hazen SL, Lefer DJ. Choline Diet and Its Gut Microbe-Derived Metabolite, Trimethylamine N-Oxide, Exacerbate Pressure Overload-Induced Heart Failure. Circ Heart Fail. 2016 Jan;9(1):e002314. PMCID:PMC4943035

Hammadah M, Georgiopoulou VV, Kalogeropoulos AP, Weber M, Wang X, Samara MA, Wu Y, Butler J, Tang WH. Elevated Soluble Fms-Like Tyrosine Kinase-1 and Placental-Like Growth Factor Levels Are Associated With Development and Mortality Risk in Heart Failure. Circ Heart Fail. 2016 Jan;9(1):e002115. PMCID:PMC4692173

Dheer R, Patterson J, Dudash M, Stachler EN, Bibby KJ, Stolz DB, Shiva S, Wang Z, Hazen SL, Barchowsky A, Stolz JF. Arsenic induces structural and compositional colonic microbiome change and promotes host nitrogen and amino acid metabolism.  Toxicol Appl Pharmacol. 2015 Dec 15;289(3):397-408. PMCID:PMC4662606

Tang WH, Hazen SL. Probiotic therapy to attenuate weight gain and trimethylamine-N-Oxide generation: A cautionary tale. Obesity (Silver Spring). 2015 Dec;23(12):2321-2. PMCID:PMC4701608

Nagatomo Y, Tang WH. Intersections Between Microbiome and Heart Failure: Revisiting the Gut Hypothesis.  J Card Fail. 2015 Dec;21(12):973-80. PMCID:PMC4666782

Kato N, Loh M, Takeuchi F et al. Trans-ancestry genome-wide association study identifies 12 genetic loci influencing blood pressure and implicates a role for DNA methylation. Nat Genet. 2015 Nov;47(11):1282-93. PMCID:PMC4719169

Kennedy DJ, Shrestha K, Sheehey B, Li XS, Guggilam A, Wu Y, Finucan M, Gabi A, Medert CM, Westfall K, Borowski A, Fedorova O, Bagrov AY, Tang WH. Elevated Plasma Marinobufagenin, An Endogenous Cardiotonic Steroid, Is Associated With Right Ventricular Dysfunction and Nitrative Stress in Heart Failure. Circ Heart Fail. 2015 Nov;8(6):1068-76. PMCID:PMC4651837
Zeltzer SM, Taylor DO, Tang WH. Long-term dietary habits and interventions in solid-organ transplantation. J Heart Lung Transplant. 2015 Nov;34(11):1357-65. PMCID:PMC4619126

Li D, Kirsop J, Tang WH. Listening to Our Gut: Contribution of Gut Microbiota and Cardiovascular Risk in Diabetes Pathogenesis. Curr Diab Rep. 2015 Sep;15(9):63. PMCID:PMC4832136

Grodin JL, Drazner MH, Dupont M, Mullens W, Taylor DO, Starling RC, Tang WH. A disproportionate elevation in right ventricular filling pressure, in relation to left ventricular filling pressure, is associated with renal impairment and increased mortality in advanced decompensated heart failure. Am Heart J. 2015 Jun;169(6):806-12. PMCID:PMC4451570

Ghosh S, Vivar J, Nelson CP, Willenborg C, Segrè AV, Mäkinen VP, Nikpay M, Erdmann J, Blankenberg S, O'Donnell C, März W, Laaksonen R, Stewart AF, Epstein SE, Shah SH, Granger CB, Hazen SL, Kathiresan S, Reilly MP, Yang X, Quertermous T, Samani NJ, Schunkert H, Assimes TL, McPherson R. Systems Genetics Analysis of Genome-Wide Association Study Reveals Novel Associations Between Key Biological Processes and Coronary Artery Disease. Arterioscler Thromb Vasc Biol. 2015 Jul;35(7):1712-22. PMCID:PMC4841833

Grodin JL, Mullens W, Dupont M, Wu Y, Taylor DO, Starling RC, Tang WH. Prognostic role of cardiac power index in ambulatory patients with advanced heart failure. Eur J Heart Fail. 2015 Jul;17(7):689-96. PMCID:PMC4676268

Airhart S, Cade WT, Jiang H, Coggan AR, Racette SL, Anderson Spearie C, Waller S, O’Connor R, Bashir A, Ory D, Schaffer JE, Novak E, Farmer M, Korenblat K, McGill JB, Dávila-Román VG, Leibowitz JL, Javidan-Nejad C, Peterson LR. A diet rich in medium-chain fatty acids improves systolic function and alters the lipidomic profile in patients with type 2 diabetes. J Clin Endocrinol (epub ahead of print).

Go YM, Walker DI, Soltow QA, Uppal K, Wachtman LM, et al. Metabolome-wide association study of phenylalanine in plasma of common marmosets. Amino Acids. 2015 Mar;47(3):589-601. PMID: 25526869; NIHMSID: NIHMS650925; PMCID: PMC4329081.

Bowler RP, Jacobson S, Cruickshank C, Hughes GJ, Siska C, Ory DS, Petrache I,  Schaffer JE, Reisdorph N, Kechris K. Plasma sphingolipids associated with chronic obstructive pulmonary disease phenotypes. Am J Respir Crit Care Med. 2015 Feb 1;191(3):275-84. PMID: 25494452; PMCID: PMC4351578.

Tang WH, Wang Z, Shrestha K, Borowski AG, Wu Y, Troughton RW, Klein AL, Hazen  SL. Intestinal microbiota-dependent phosphatidylcholine metabolites, diastolic dysfunction, and adverse clinical outcomes in chronic systolic heart failure. J Card Fail. 2015 Feb;21(2):91-6. PMID: 25459686; PMCID: PMC4312712.

Tang WH, Wang Z, Kennedy DJ, Wu Y, Buffa JA, Agatisa-Boyle B, Li XS, Levison BS, Hazen SL. Gut microbiota-dependent trimethylamine N-oxide (TMAO) pathway contributes to both development of renal insufficiency and mortality risk in chronic kidney disease. Circ Res. 2015 Jan 30;116(3):448-55. PMID: 25599331; PMCID: PMC4312512.

Go YM, Kim CW, Walker DI, Kang DW, Kumar S, et al. Disturbed f low induces systemic changes in metabolites in mouse plasma: a metabolomics study using ApoE-/- mice with partial carotid ligation. Am J Physiol Regul Int egr Comp Physiol. 2015 Jan 1;308(1):R62-72. PMID: 25377480; PMCID: PMC4281678.

Yu T, Bai Y. Network-based modular latent structure analysis. BMC Bioinformatics. 2014 Nov 13;15 Suppl 13:S6. PMID: 25435002; PMCID: PMC4248660.

Patel RM, Roback JD, Uppal K, Yu T, Jones DP, et al. Metabolomics profile comparisons of irradiated and nonirradiated stored donor red blood cells. Transfusion. 2014 Oct 21; PMID: 25330719; NIHMSID: NIHMS659208

Yu T, Jones DP. Improving peak detection in high-resolution LC/MS metabolomics data using preexisting knowledge and machine learning approach. Bioinformatics. 2014 Oct 15;30(20):2941-8. PMID: 25005748; PMCID: PMC4184266.

Kumar S, Kim CW, Simmons RD, Jo H. Role of f low-sensitive microRNAs in endothelial dysfunction and atherosclerosis: mechanosensitive athero-miRs. Arterioscler Thromb Vasc Biol. 2014 Oct;34(10):2206-16. PMID: 25012134; NIHMSID: NIHMS610187; PMCID: PMC4169332.

Singh A, Agarwal R, Diaz-Ruiz CA, Willett NJ, Wang P, et al. Nanoengineered particles for enhanced intra-articular retention and delivery of proteins. Adv Healthc Mater. 2014 Oct;3(10):1562-7, 1525. PMID: 24687997; NIHMSID: NIHMS584789; PMCID: PMC4182168.

Alvarez JA, Chowdhury R, Jones DP, Martin GS, Brigham KL, et al. Vitamin D status is independently associated with plasma glutathione and cysteine thiol/disulphide redox status in adults. Clin Endocrinol (Oxf). 2014 Sep;81(3):458-66. PMID: 24628365; NIHMSID: NIHMS574031; PMCID: PMC4115025.

Dunn J, Qiu H, Kim S, Jjingo D, Hoffman R, et al. Flow-dependent epigenetic DNA methylation regulates endothelial gene expression and atherosclerosis. J Clin Invest . 2014 Jul;124(7):3187-99. PMID: 24865430; PMCID: PMC4071393.

Kim CW, Kumar S, Son DJ, Jang IH, Griendling KK, et al. Prevention of abdominal aortic aneurysm by anti-microRNA-712 or anti-microRNA-205 in angiotensin II-inf used mice. Arterioscler Thromb Vasc Biol. 2014 Jul;34(7):1412-21. PMID: 24812324; NIHMSID: NIHMS590593; PMCID: PMC4111131.

Cruickshank-Quinn, C. Quinn, Kevin D., Powell, R., Yang, Y., Armstrong, M., Mahaffey, S., Reisdorph, R., Reisdorph, N. Multi-step preparation technique to recover multiple metabolite compound classes for in-depth and informative metabolomic analysis. Journal of Visualization Experiments. 2014 Jul 11;(89).

Cruickshank-Quinn, C. Mahaffey, S., Justice, M.J., Hughes, G., Armstrong, M., Kechris, K., Bowler, R., Reisdorph, R., Petrache, I., Reisdorph, N. Transient and persistent metabolomic changes in plasma following chronic cigarette smoke exposure in a mouse model.  PloS One.  2014 Jul 9;9(7).

Ghasemzadeh N, Patel RS, Eapen DJ, Veledar E, Al Kassem H, et al. Oxidative stress is associated with increased pulmonary artery systolic pressure in humans. Hypertension. 2014 Jun;63(6):1270- 5. PMID: 24614216; NIHMSID: NIHMS567602; PMCID: PMC4138535.

Cribbs SK, Park Y, Guidot DM, Martin GS, Brown LA, et al. Metabolomics of bronchoalveolar lavage differentiate healthy HIV-1-inf ected subjects f rom controls. AIDS Res Hum Retroviruses. 2014 Jun;30(6):579-85. PMID: 24417396; PMCID: PMC4046199.

Huang Y. Bootstrap for the case-cohort design. Biometrika. 2014 Jun;101(2):465-476. PMID: 25170175; NIHMSID: NIHMS603005; PMCID: PMC4143157.

Headen DM, Aubry G, Lu H, García AJ. Microfluidic-based generation of size-controlled, biofunctionalized synthetic polymer microgels for cell encapsulation. Adv Mater. 2014 May 21;26(19):3003-8. PMID: 24615922; NIHMSID: NIHMS584798; PMCID: PMC4058833.

Yang R, Bai Y, Qin Z, Yu T. EgoNet: identification of human disease ego-network modules. BMC Genomics. 2014 Apr 28;15:314. PMID: 24773628; PMCID: PMC4234496.

Nagaraja MP, Jo H. The Role of Mechanical Stimulation in Recovery of Bone Loss-High versus Low Magnitude and Frequency of Force. Life (Basel). 2014 Apr 2;4(2):117-30. PMID: 25370188; PMCID: PMC4187165.

Ni CW, Kumar S, Ankeny CJ, Jo H. Development of immortalized mouse aortic endothelial cell lines. Vasc Cell. 2014 Apr 1;6(1):7. PMID: 24690145; PMCID: PMC4230636.

Go YM, Roede JR, Orr M, Liang Y, Jones DP. Integrated redox proteomics and metabolomics of mitochondria to identify mechanisms of cd toxicity. Toxicol Sci.  2014 May;139(1):59-73. PMID:  24496640; PMCID: PMC4007108.

Tarbell JM, Shi ZD, Dunn J, Jo H. Fluid Mechanics, Arterial Disease, and Gene Expression. Annu Rev Fluid Mech. 2014 Jan;46:591-614. PMID: 25360054; NIHMSID: NIHMS623399; PMCID: PMC4211638.

Frediani JK, Jones DP, Tukvadze N, Uppal K, Sanikidze E, et al. Plasma metabolomics in human pulmonary tuberculosis disease: a pilot study. PLoS One. 2014;9(10):e108854. PMID: 25329995; PMCID: PMC4198093.

Go YM, Jones DP. Redox biology: interface of the exposome with the proteome, epigenome and genome. Redox Biol. 2014;2:358-60. PMID: 24563853; PMCID: PMC3926118.

Tang WHW, Wang Z, Fan Y, Levison B, Hazen JE, Donahue LM, Wu Y, Hazen SL. Prognostic value of elevated levels of intestinal microbe-generated metabolite, trimethylamine-N-oxide, in patients with heart failure: Refining the gut hypothesis. Journal of the American College of Cardiology. (2014) 64(18):1908-14.

Koeth RA, Levison BS, Culley MK, Buffa JA, Wang Z, Gregory JC, Org E, Wu Y, Li L, Smith JD, Tang WH, DiDonato JA, Lusis AJ, Hazen SL. γ-Butyrobetaine is a proatherogenic intermediate in gut microbial metabolism of L-carnitine to TMAO. Cell Metabolism (2014) 20(5):799-812.

Hughes, G., C. Cruickshank-Quinn, R. Reisdorph, S. Lutz, I. Petrache, N. Reisdorph, R. Bowler and K. Kechris. MS Prep Summarization, normalization and diagnostics for processing of mass spectrometry-based metabolomic data. Bioinformatics 2014.  30(1): 133-134. PMCID: PMC386654

Go YM, Uppal K, Walker DI, Tran V, Dury L, et al. Mitochondrial metabolomics using high-resolution Fourier-transform mass spectrometry. Methods Mol Biol. 2014;1198:43-73. PMID: 25270922; NIHMSID: NIHMS659198; PMCID: PMC4318503.

Go YM, Son DJ, Park H, Orr M, Hao L, et al. Disturbed f low enhances inf lammatory signaling and atherogenesis by increasing thioredoxin-1 level in endothelial cell nuclei. PLoS One. 2014;9(9):e108346. PMID: 25265386; PMCID: PMC4180949.

Jiang H, Hsu FF, Farmer MS, Peterson LR, Schaffer JE, Ory DS, Jiang X. Development and validation of LC-MS/MS method for determination of very long acyl chain (C22:0 and C24:0) ceramides in human plasma. Anal Bioanal Chem. 2013 Sep;405(23):7357-65. PMID: 23857140; PMCID: PMC3766747.

Li S, Park Y, Duraisingham S, Strobel FH, Khan N, Soltow QA, Jones DP, Pulendran B., Predicting network activity from high throughput metabolomics. PLoS Comput Biol. 2013 Jul;9(7):e1003123. PMID: 23861661; PMCID: PMC3701697.

Yang, Y., C. Cruickshank, M. Armstrong, S. Mahaffey, R. Reisdorph and N. Reisdorph.  New sample preparation approach for mass spectrometry-based profiling of plasma results in improved coverage of metabolome. J Chromatogr A 2013. 1300: 217-226. PMCID: PMC3734953.