Abstract
Metabolomics has been increasingly applied to study renal and related cardiometabolic diseases, including diabetes and cardiovascular diseases. These studies span cross-sectional studies correlating metabolites with specific phenotypes, longitudinal studies to identify metabolite predictors of future disease, and physiologic/interventional studies to probe underlying causal relationships. This chapter provides a description of how metabolomic profiling is being used in these contexts, with an emphasis on study design considerations as a practical guide for investigators who are new to this area. Research in kidney diseases is underlined to illustrate key principles. The chapter concludes by discussing the future potential of metabolomics in the study of renal and cardiometabolic diseases.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Thygesen K, Alpert JS, Jaffe AS, Chaitman BR, Bax JJ, Morrow DA, White HD, Executive Group on behalf of the Joint European Society of Cardiology/American College of Cardiology/American Heart Association/World Heart Federation Task Force for the Universal Definition of Myocardial I (2018) Fourth universal definition of myocardial infarction (2018). Glob Heart 13(4):305–338. https://doi.org/10.1016/j.gheart.2018.08.004
Anderson KM, Odell PM, Wilson PW, Kannel WB (1991) Cardiovascular disease risk profiles. Am Heart J 121(1 Pt 2):293–298
Goff DC Jr, Lloyd-Jones DM, Bennett G, Coady S, D’Agostino RB, Gibbons R, Greenland P, Lackland DT, Levy D, O’Donnell CJ, Robinson JG, Schwartz JS, Shero ST, Smith SC Jr, Sorlie P, Stone NJ, Wilson PW, Jordan HS, Nevo L, Wnek J, Anderson JL, Halperin JL, Albert NM, Bozkurt B, Brindis RG, Curtis LH, De Mets D, Hochman JS, Kovacs RJ, Ohman EM, Pressler SJ, Sellke FW, Shen WK, Smith SC Jr, Tomaselli GF, American College of Cardiology/American Heart Association Task Force on Practice G (2014) 2013 ACC/AHA guideline on the assessment of cardiovascular risk: a report of the American College of Cardiology/American Heart Association task force on practice guidelines. Circulation 129(25 Suppl 2):S49–S73. https://doi.org/10.1161/01.cir.0000437741.48606.98
Kidney Disease: Improving Global Outcomes (KDIGO) (2013) KDIGO clinical practice guideline for the evaluation and management of chronic kidney disease. Kidney Int 3(1):1–150
Inker LA, Schmid CH, Tighiouart H, Eckfeldt JH, Feldman HI, Greene T, Kusek JW, Manzi J, Van Lente F, Zhang YL, Coresh J, Levey AS, Chronic Kidney Disease Epidemiology Collaboration Investigators (2012) Estimating glomerular filtration rate from serum creatinine and cystatin C. N Engl J Med 367(1):20–29. https://doi.org/10.1056/NEJMoa1114248
Levey AS, Inker LA, Matsushita K, Greene T, Willis K, Lewis E, De Zeeuw D, Cheung AK, Coresh J (2014) GFR decline as an endpoint for clinical trials in CKD: a scientific workshop sponsored by the National Kidney Foundation and the US Food and Drug Administration. Am J Kidney Dis 64(6):821–835
Stevens LA, Coresh J, Greene T, Levey AS (2006) Assessing kidney function--measured and estimated glomerular filtration rate. N Engl J Med 354(23):2473–2483. https://doi.org/10.1056/NEJMra054415
Stevens LA, Schmid CH, Greene T, Li L, Beck GJ, Joffe MM, Froissart M, Kusek JW, Zhang YL, Coresh J, Levey AS (2009) Factors other than glomerular filtration rate affect serum cystatin C levels. Kidney Int 75(6):652–660. https://doi.org/10.1038/ki.2008.638
HJL H, Greene T, Tighiouart H, Gansevoort RT, Coresh J, Simon AL, Chan TM, Hou FF, Lewis JB, Locatelli F, Praga M, Schena FP, Levey AS, Inker LA, Chronic Kidney Disease Epidemiology C (2019) Change in albuminuria as a surrogate endpoint for progression of kidney disease: a meta-analysis of treatment effects in randomised clinical trials. Lancet Diabetes Endocrinol 7(2):128–139. https://doi.org/10.1016/S2213-8587(18)30314-0
Coresh J, Heerspink HJL, Sang Y, Matsushita K, Arnlov J, Astor BC, Black C, Brunskill NJ, Carrero JJ, Feldman HI, Fox CS, Inker LA, Ishani A, Ito S, Jassal S, Konta T, Polkinghorne K, Romundstad S, Solbu MD, Stempniewicz N, Stengel B, Tonelli M, Umesawa M, Waikar SS, Wen CP, Wetzels JFM, Woodward M, Grams ME, Kovesdy CP, Levey AS, Gansevoort RT, Chronic Kidney Disease Prognosis C, Chronic Kidney Disease Epidemiology C (2019) Change in albuminuria and subsequent risk of end-stage kidney disease: an individual participant-level consortium meta-analysis of observational studies. Lancet Diabetes Endocrinol 7(2):115–127. https://doi.org/10.1016/S2213-8587(18)30313-9
Inker LA, Levey AS, Pandya K, Stoycheff N, Okparavero A, Greene T, Chronic Kidney Disease Epidemiology C (2014) Early change in proteinuria as a surrogate end point for kidney disease progression: an individual patient meta-analysis. Am J Kidney Dis 64(1):74–85. https://doi.org/10.1053/j.ajkd.2014.02.020
Waikar SS, Rebholz CM, Zheng Z, Hurwitz S, Hsu CY, Feldman HI, Xie D, Liu KD, Mifflin TE, Eckfeldt JH, Kimmel PL, Vasan RS, Bonventre JV, Inker LA, Coresh J, Chronic Kidney Disease Biomarkers Consortium I (2018) Biological variability of estimated GFR and albuminuria in CKD. Am J Kidney Dis 72(4):538–546. https://doi.org/10.1053/j.ajkd.2018.04.023
Schrimpe-Rutledge AC, Codreanu SG, Sherrod SD, McLean JA (2016) Untargeted metabolomics strategies-challenges and emerging directions. J Am Soc Mass Spectrom 27(12):1897–1905. https://doi.org/10.1007/s13361-016-1469-y
Rhee EP, Waikar SS, Rebholz CM, Zheng Z, Perichon R, Clish CB, Evans AM, Avila J, Denburg MR, Anderson AH, Vasan RS, Feldman HI, Kimmel PL, Coresh J, Consortium CKDB (2019) Variability of two metabolomic platforms in CKD. Clin J Am Soc Nephrol 14(1):40–48. https://doi.org/10.2215/CJN.07070618
Mahieu NG, Patti GJ (2017) Systems-level annotation of a metabolomics data set reduces 25000 features to fewer than 1000 unique metabolites. Anal Chem 89(19):10397–10406. https://doi.org/10.1021/acs.analchem.7b02380
Sekula P, Goek ON, Quaye L, Barrios C, Levey AS, Romisch-Margl W, Menni C, Yet I, Gieger C, Inker LA, Adamski J, Gronwald W, Illig T, Dettmer K, Krumsiek J, Oefner PJ, Valdes AM, Meisinger C, Coresh J, Spector TD, Mohney RP, Suhre K, Kastenmuller G, Kottgen A (2016) A metabolome-wide association study of kidney function and disease in the general population. J Am Soc Nephrol 27(4):1175–1188. https://doi.org/10.1681/ASN.2014111099
Ho JE, Larson MG, Ghorbani A, Cheng S, Chen MH, Keyes M, Rhee EP, Clish CB, Vasan RS, Gerszten RE, Wang TJ (2016) Metabolomic profiles of body mass index in the Framingham heart study reveal distinct Cardiometabolic phenotypes. PLoS One 11(2):e0148361. https://doi.org/10.1371/journal.pone.0148361
Newgard CB, An J, Bain JR, Muehlbauer MJ, Stevens RD, Lien LF, Haqq AM, Shah SH, Arlotto M, Slentz CA, Rochon J, Gallup D, Ilkayeva O, Wenner BR, Yancy WS Jr, Eisenson H, Musante G, Surwit RS, Millington DS, Butler MD, Svetkey LP (2009) A branched-chain amino acid-related metabolic signature that differentiates obese and lean humans and contributes to insulin resistance. Cell Metab 9(4):311–326. https://doi.org/10.1016/j.cmet.2009.02.002
Kastenmuller G, Raffler J, Gieger C, Suhre K (2015) Genetics of human metabolism: an update. Hum Mol Genet 24(R1):R93–R101. https://doi.org/10.1093/hmg/ddv263
Sekula P, Del Greco MF, Pattaro C, Kottgen A (2016) Mendelian randomization as an approach to assess causality using observational data. J Am Soc Nephrol 27(11):3253–3265. https://doi.org/10.1681/ASN.2016010098
Rhee EP, Clish CB, Wenger J, Roy J, Elmariah S, Pierce KA, Bullock K, Anderson AH, Gerszten RE, Feldman HI (2016) Metabolomics of chronic kidney disease progression: a case-control analysis in the chronic renal insufficiency cohort study. Am J Nephrol 43(5):366–374. https://doi.org/10.1159/000446484
Krug S, Kastenmuller G, Stuckler F, Rist MJ, Skurk T, Sailer M, Raffler J, Romisch-Margl W, Adamski J, Prehn C, Frank T, Engel KH, Hofmann T, Luy B, Zimmermann R, Moritz F, Schmitt-Kopplin P, Krumsiek J, Kremer W, Huber F, Oeh U, Theis FJ, Szymczak W, Hauner H, Suhre K, Daniel H (2012) The dynamic range of the human metabolome revealed by challenges. FASEB J 26(6):2607–2619. https://doi.org/10.1096/fj.11-198093
Scalbert A, Brennan L, Manach C, Andres-Lacueva C, Dragsted LO, Draper J, Rappaport SM, van der Hooft JJ, Wishart DS (2014) The food metabolome: a window over dietary exposure. Am J Clin Nutr 99(6):1286–1308. https://doi.org/10.3945/ajcn.113.076133
Guasch-Ferre M, Bhupathiraju SN, Hu FB (2018) Use of metabolomics in improving assessment of dietary intake. Clin Chem 64(1):82–98. https://doi.org/10.1373/clinchem.2017.272344
Garcia-Perez I, Posma JM, Gibson R, Chambers ES, Hansen TH, Vestergaard H, Hansen T, Beckmann M, Pedersen O, Elliott P, Stamler J, Nicholson JK, Draper J, Mathers JC, Holmes E, Frost G (2017) Objective assessment of dietary patterns by use of metabolic phenotyping: a randomised, controlled, crossover trial. Lancet Diabetes Endocrinol 5(3):184–195. https://doi.org/10.1016/S2213-8587(16)30419-3
Tolstikov V (2016) Metabolomics: bridging the gap between pharmaceutical development and population health. Metabolites 6(3):E20. https://doi.org/10.3390/metabo6030020
Lewis GD, Wei R, Liu E, Yang E, Shi X, Martinovic M, Farrell L, Asnani A, Cyrille M, Ramanathan A, Shaham O, Berriz G, Lowry PA, Palacios IF, Tasan M, Roth FP, Min J, Baumgartner C, Keshishian H, Addona T, Mootha VK, Rosenzweig A, Carr SA, Fifer MA, Sabatine MS, Gerszten RE (2008) Metabolite profiling of blood from individuals undergoing planned myocardial infarction reveals early markers of myocardial injury. J Clin Investig 118(10):3503–3512. https://doi.org/10.1172/JCI35111
Rhee EP, Clish CB, Ghorbani A, Larson MG, Elmariah S, McCabe E, Yang Q, Cheng S, Pierce K, Deik A, Souza AL, Farrell L, Domos C, Yeh RW, Palacios I, Rosenfield K, Vasan RS, Florez JC, Wang TJ, Fox CS, Gerszten RE (2013) A combined epidemiologic and metabolomic approach improves CKD prediction. J Am Soc Nephrol 24(8):1330–1338. https://doi.org/10.1681/ASN.2012101006
Curtin F, Schulz P (1998) Multiple correlations and Bonferroni’s correction. Biol Psychiatry 44(8):775–777
Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate - a practical and powerful approach to multiple testing. J R Stat Soc B 57(1):289–300
Niewczas MA, Sirich TL, Mathew AV, Skupien J, Mohney RP, Warram JH, Smiles A, Huang X, Walker W, Byun J, Karoly ED, Kensicki EM, Berry GT, Bonventre JV, Pennathur S, Meyer TW, Krolewski AS (2014) Uremic solutes and risk of end-stage renal disease in type 2 diabetes: metabolomic study. Kidney Int 85(5):1214–1224. https://doi.org/10.1038/ki.2013.497
Warren B, Rebholz CM, Sang Y, Lee AK, Coresh J, Selvin E, Grams ME (2018) Diabetes and trajectories of estimated glomerular filtration rate: a prospective cohort analysis of the atherosclerosis risk in communities study. Diabetes Care 41(8):1646–1653. https://doi.org/10.2337/dc18-0277
Bell EK, Gao L, Judd S, Glasser SP, McClellan W, Gutierrez OM, Safford M, Lackland DT, Warnock DG, Muntner P (2012) Blood pressure indexes and end-stage renal disease risk in adults with chronic kidney disease. Am J Hypertens 25(7):789–796. https://doi.org/10.1038/ajh.2012.48
Yin X, Subramanian S, Willinger CM, Chen G, Juhasz P, Courchesne P, Chen BH, Li X, Hwang SJ, Fox CS, O’Donnell CJ, Muntendam P, Fuster V, Bobeldijk-Pastorova I, Sookoian SC, Pirola CJ, Gordon N, Adourian A, Larson MG, Levy D (2016) Metabolite signatures of metabolic risk factors and their longitudinal changes. J Clin Endocrinol Metab 101(4):1779–1789. https://doi.org/10.1210/jc.2015-2555
Bhupathiraju SN, Guasch-Ferre M, Gadgil MD, Newgard CB, Bain JR, Muehlbauer MJ, Ilkayeva OR, Scholtens DM, Hu FB, Kanaya AM, Kandula NR (2018) Dietary patterns among Asian Indians living in the United States have distinct Metabolomic profiles that are associated with Cardiometabolic risk. J Nutr 148(7):1150–1159. https://doi.org/10.1093/jn/nxy074
Ramezani A, Raj DS (2014) The gut microbiome, kidney disease, and targeted interventions. J Am Soc Nephrol 25(4):657–670. https://doi.org/10.1681/ASN.2013080905
Coresh J, Inker LA, Sang Y, Chen J, Shafi T, Post WS, Shlipak MG, Ford L, Goodman K, Perichon R, Greene T, Levey AS (2018) Metabolomic profiling to improve glomerular filtration rate estimation: a proof-of-concept study. Nephrol Dial Transplant 34(5):825–833. https://doi.org/10.1093/ndt/gfy094
Titan SM, Venturini G, Padilha K, Tavares G, Zatz R, Bensenor I, Lotufo PA, Rhee EP, Thadhani RI, Pereira AC (2019) Metabolites related to eGFR: evaluation of candidate molecules for GFR estimation using untargeted metabolomics. Clin Chim Acta 489:242–248. https://doi.org/10.1016/j.cca.2018.08.037
Goek ON, Doring A, Gieger C, Heier M, Koenig W, Prehn C, Romisch-Margl W, Wang-Sattler R, Illig T, Suhre K, Sekula P, Zhai G, Adamski J, Kottgen A, Meisinger C (2012) Serum metabolite concentrations and decreased GFR in the general population. Am J Kidney Dis 60(2):197–206. https://doi.org/10.1053/j.ajkd.2012.01.014
Ng DP, Salim A, Liu Y, Zou L, Xu FG, Huang S, Leong H, Ong CN (2012) A metabolomic study of low estimated GFR in non-proteinuric type 2 diabetes mellitus. Diabetologia 55(2):499–508. https://doi.org/10.1007/s00125-011-2339-6
Luo S, Coresh J, Tin A, Rebholz CM, Appel LJ, Chen J, Vasan RS, Anderson AH, Feldman HI, Kimmel PL, Waikar SS, Kottgen A, Evans AM, Levey AS, Inker LA, Sarnak MJ, Grams ME, Chronic Kidney Disease Biomarkers Consortium I (2019) Serum Metabolomic alterations associated with proteinuria in CKD. Clin J Am Soc Nephrol 14(3):342–353. https://doi.org/10.2215/CJN.10010818
Guo L, Milburn MV, Ryals JA, Lonergan SC, Mitchell MW, Wulff JE, Alexander DC, Evans AM, Bridgewater B, Miller L, Gonzalez-Garay ML, Caskey CT (2015) Plasma metabolomic profiles enhance precision medicine for volunteers of normal health. Proc Natl Acad Sci U S A 112(35):E4901–E4910. https://doi.org/10.1073/pnas.1508425112
Krebs-Smith SM, Pannucci TE, Subar AF, Kirkpatrick SI, Lerman JL, Tooze JA, Wilson MM, Reedy J (2018) Update of the healthy eating index: HEI-2015. J Acad Nutr Diet 118(9):1591–1602. https://doi.org/10.1016/j.jand.2018.05.021
Grant LK, Ftouni S, Nijagal B, De Souza DP, Tull D, McConville MJ, Rajaratnam SMW, Lockley SW, Anderson C (2019) Circadian and wake-dependent changes in human plasma polar metabolites during prolonged wakefulness: a preliminary analysis. Sci Rep 9(1):4428. https://doi.org/10.1038/s41598-019-40353-8
Breier M, Wahl S, Prehn C, Fugmann M, Ferrari U, Weise M, Banning F, Seissler J, Grallert H, Adamski J, Lechner A (2014) Targeted metabolomics identifies reliable and stable metabolites in human serum and plasma samples. PLoS One 9(2):e89728. https://doi.org/10.1371/journal.pone.0089728
Wedge DC, Allwood JW, Dunn W, Vaughan AA, Simpson K, Brown M, Priest L, Blackhall FH, Whetton AD, Dive C, Goodacre R (2011) Is serum or plasma more appropriate for intersubject comparisons in metabolomic studies? An assessment in patients with small-cell lung cancer. Anal Chem 83(17):6689–6697. https://doi.org/10.1021/ac2012224
Lin Z, Zhang Z, Lu H, Jin Y, Yi L, Liang Y (2014) Joint MS-based platforms for comprehensive comparison of rat plasma and serum metabolic profiling. Biomed Chromatogr 28(9):1235–1245. https://doi.org/10.1002/bmc.3152
Ishikawa M, Tajima Y, Murayama M, Senoo Y, Maekawa K, Saito Y (2013) Plasma and serum from nonfasting men and women differ in their lipidomic profiles. Biol Pharm Bull 36(4):682–685
Brunner MP, Shah SH, Craig DM, Stevens RD, Muehlbauer MJ, Bain JR, Newgard CB, Kraus WE, Granger CB, Sketch MH Jr, Newby LK (2011) Effect of heparin administration on metabolomic profiles in samples obtained during cardiac catheterization. Circ Cardiovasc Genet 4(6):695–700. https://doi.org/10.1161/CIRCGENETICS.111.960575
Gika HG, Theodoridis GA, Wilson ID (2008) Liquid chromatography and ultra-performance liquid chromatography-mass spectrometry fingerprinting of human urine: sample stability under different handling and storage conditions for metabonomics studies. J Chromatogr A 1189(1–2):314–322. https://doi.org/10.1016/j.chroma.2007.10.066
Teahan O, Gamble S, Holmes E, Waxman J, Nicholson JK, Bevan C, Keun HC (2006) Impact of analytical bias in metabonomic studies of human blood serum and plasma. Anal Chem 78(13):4307–4318. https://doi.org/10.1021/ac051972y
Anton G, Wilson R, Yu ZH, Prehn C, Zukunft S, Adamski J, Heier M, Meisinger C, Romisch-Margl W, Wang-Sattler R, Hveem K, Wolfenbuttel B, Peters A, Kastenmuller G, Waldenberger M (2015) Pre-analytical sample quality: metabolite ratios as an intrinsic marker for prolonged room temperature exposure of serum samples. PLoS One 10(3):e0121495. https://doi.org/10.1371/journal.pone.0121495
Kottgen A, Raffler J, Sekula P, Kastenmuller G (2018) Genome-wide association studies of metabolite concentrations (mGWAS): relevance for nephrology. Semin Nephrol 38(2):151–174. https://doi.org/10.1016/j.semnephrol.2018.01.009
Tzoulaki I, Ebbels TM, Valdes A, Elliott P, Ioannidis JP (2014) Design and analysis of metabolomics studies in epidemiologic research: a primer on -omic technologies. Am J Epidemiol 180(2):129–139. https://doi.org/10.1093/aje/kwu143
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Rebholz, C.M., Rhee, E.P. (2020). Application of Metabolomics to Renal and Cardiometabolic Diseases. In: Li, S. (eds) Computational Methods and Data Analysis for Metabolomics. Methods in Molecular Biology, vol 2104. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0239-3_20
Download citation
DOI: https://doi.org/10.1007/978-1-0716-0239-3_20
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-0238-6
Online ISBN: 978-1-0716-0239-3
eBook Packages: Springer Protocols