1H NMR metabonomics of plasma lipoprotein subclasses: Elucidation of metabolic clustering by self-organising maps

NMR in Biomedicine

Volumn 20, Issue 7, 2007, Pages 658-672

  Suna, Teemu ^a   Salminen, Aino ^a   Soininen, Pasi ^b   Laatikainen, Reino ^b   Ingman, Petri ^c   Mäkelä, Sanna ^d   Savolainen, Markku J ^d   Hannuksela, Minna L ^d   Jauhiainen, Matti ^e   Taskinen, Marja Riitta ^f   Kaski, Kimmo ^a   Ala Korpela, Mika ^a  

^a AALTO UNIVERSITY   (Finland)

^b UNIVERSITY OF EASTERN FINLAND   (Finland)

^c UNIVERSITY OF TURKU   (Finland)

^d UNIVERSITY OF OULU   (Finland)

^e BIOMEDICUM HELSINKI   (Finland)

^f UNIVERSITY OF HELSINKI   (Finland)

Author keywords

1H NMR metabonomics; Cholesterol; Coronary heart disease; Lipoprotein subclass; Metabolic clustering; Plasma; Self organising map; Serum

Indexed keywords

METABOLISM; NUCLEAR MAGNETIC RESONANCE; PLASMA (HUMAN); SELF ORGANIZING MAPS;

ELUCIDATION; LIPOPROTEIN; METABOLIC CLUSTERING;

PROTEINS;

CHOLESTEROL; HIGH DENSITY LIPOPROTEIN; INTERMEDIATE DENSITY LIPOPROTEIN; LIPOPROTEIN; LOW DENSITY LIPOPROTEIN; VERY LOW DENSITY LIPOPROTEIN; CHOLINE; PROTON;

ARTICLE; ARTIFICIAL NEURAL NETWORK; BLOOD SAMPLING; CLUSTER ANALYSIS; DIAGNOSTIC ACCURACY; GENE CLUSTER; GENOMICS; HUMAN; HYPERLIPIDEMIA; LIPID ANALYSIS; LIPID METABOLISM; LIPOPROTEIN BLOOD LEVEL; LIPOPROTEIN METABOLISM; MASS SPECTROMETRY; METABONOMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRACTICE GUIDELINE; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROTON NUCLEAR MAGNETIC RESONANCE; QUANTITATIVE ANALYSIS; RELIABILITY; BLOOD; CLASSIFICATION; METABOLISM; METHODOLOGY;

CHOLINE; HUMANS; LIPOPROTEINS; MAGNETIC RESONANCE SPECTROSCOPY; PROTONS;

EID: 36248937204     PISSN: 09523480     EISSN: 10991492     Source Type: Journal    
DOI: 10.1002/nbm.1123     Document Type: Article

References (69)

1. Nicholson JK, Wilson ID. Understanding 'global' systems biology: metabonomics and the continuum of metabolism. Nat. Rev. Drug Disc. 2003; 2: 668-676.
2. Fernie AF, Trethewey RN, Krotzky AJ, Willmitzer L. Metabolite profiling: from diagnostics to systems biology. Nat. Rev. Mol. Cell Biol. 2004; 5: 1-7.
3. 1H NMR spectroscopy of human blood plasma. Prog. Nucl. Magn. Reson. Spectrosc. 1995; 27: 475-554.
4. Haykin S. Neural networks. A comprehensive foundation. Second edition. Prentice Hall International: Upper Saddle River, NJ, 1999.
5. Haydon GH, Jalan R, Ala-Korpela M, Hiltunen Y, Hanley J, Jarvis LM, Ludlam CA, Hayes PC. Prediction of cirrhosis in patients with chronic hepatitis C infection by artificial neural network analysis of virus and clinical factors. J. Viral Hepat. 1998; 5: 255-264.
6. Väänänen T, Koskela H, Hiltunen Y, Ala-Korpela M. Application of quantitative artificial neural network analysis to 2D NMR spectra of hydrocarbon mixtures. J. Chem. Inf. Comput. Sci. 2002; 42: 1343-1346.
7. 1H NMR spectra of urine using an artificial neural network. J. Pharm. Biomed. Anal. 1995; 13: 205-211.
8. 1H NMR data from human blood plasma. J. Magn. Reson. B 1995; 106: 191-194.
9. 1H NMR data of human plasma. NMR Biomed. 1995; 8: 235-244.
10. 1H NMR spectra. J. Magn. Reson. 1998; 134: 176-179.
11. 1H NMR magnitude spectra using automated artificial neural network analysis. J. Magn. Reson. 2002; 154: 1-5.
12. Holmes E, Nicholson JK, Tranter G. Metabonomic characterization of genetic variations in toxicological and metabolic responses using probabilistic neural networks. Chem. Res. Toxicol. 2001; 14: 182-191.
13. Ott KH, Araníbar N, Singh B, Stockton GW. Metabonomics classifies pathways affected by bioactive compounds. Artificial neural network classification of NMR spectra of plant extracts. Phytochemistry 2003; 62: 971-985.
14. Kohonen T. Self-organized maps. Springer-Verlag: Berlin, 1995.
15. Kohonen T, Hynninen J, Kangas J, Laaksonen J. SOM PAK: the self-organizing map program package, Report A31. Helsinki University of Technology, Laboratory of Computer and Information Science, Espoo, Finland, 1996.
16. Hyvönen MT, Hiltunen Y, El-Deredy W, Ojala T, Vaara J, Kovanen PT, Ala-Korpela M. Application of self-organizing maps in conformational analysis of lipids. J Am. Chem. Soc. 2001; 123: 810-816.
17. Nikkilä J, Törönen P, Kaski S, Venna J, Castrén E, Wong G. Analysis and visualization of gene expression data using self-organizing maps. Neural Networks 2002; 15: 953-966.
18. Kalelkar S, Dow ER, Grimes J, Claphain M, Hu H. Automated analysis of proton NMR spectra from combinatorial rapid parallel synthesis using self-organizing maps. J. Comb. Chem. 2002; 4: 622-629.
19. Haydon GH, Hiltunen Y, Lucey MR, Collett D, Gunson B, Murphy N, Nightingale PG, Neuberger J. Self-organizing maps can determine outcome and match recipients and donors at orthotopic liver transplantation. Transplantation 2005; 79: 213-218.
20. Nattkemper TW, Wismüller A. Tumor feature visualization with unsupervised leaming. Med. Image Anal. 2005; 9: 344-351.
21. 1H-NMR spectroscopy and self-organizing maps. NMR Biomed. 2003; 16: 1-11.
22. 1H NMR spectroscopy data. NMR Biomed. 1998; 11: 168-176.
23. Carmena R, Duriez P, Fruchart JC. Atherogenic lipoprotein particles in atherosclerosis. Circulation 2004; 109: III-2-III-7.
24. Ala-Korpela M, Sipola P, Kaski K. Characterization and molecular detection of atherothrombosis by magnetic resonance - potential tools for individual risk assessment and diagnostics. Ann. Med. 2006; 38: 322-336.
25. 1H NMR-based absolute quantitation of human lipoproteins and their lipid contents directly from plasma. J. Lipid Res. 1994; 35: 2292-2304.
26. 1H NMR studies of human blood plasma. FEBS Lett. 1987; 219: 239-243.
27. Otvos JD, Jeyarajah EJ, Hayes LW, Freedman DS, Janjan NA, Anderson T. Relationships between the proton nuclear magnetic resonance properties of plasma lipoproteins and cancer. Clin. Chem. 1991; 37: 369-376.
28. Engan T, Bjerve KS, Høe AL, Krane J. Proton magnetic resonance spectroscopy of fractionated plasma lipoproteins and reconstituted plasma from healthy subjects and patients with cancer. Scand. J. Clin. Lab. Invest. 1992; 52: 393-408.
29. Serrai H, Nadal L, Leray G, Leroy B, Delplanque B, de Certaines JD. Quantification of plasma lipoprotein fractions by wavelet transform time-domain data processing of the proton nuclear magnetic resonance methylene spectral region. NMR Biomed. 1998; 11: 273-280.
30. Bathen TF, Engan T, Krane J. Principal component analysis of proton nuclear magnetic resonance spectra of lipoprotein fractions from patients with coronary heart disease and healthy subjects. Scand. J. Clin. Lab. Invest. 1999; 59: 349-360.
31. Bathen TF, Krane J, Engan T, Bjerve KS, Axelson D. Quantification of plasma lipids and apolipoproteins by use of proton NMR spectroscopy, multivariate and neural network analysis. NMR Biomed. 2000; 13: 271-288.
32. Taskinen MR, Packard CJ, Shepherd J. Effect of insulin therapy on metabolic fate of apolipoprotein B-containing lipoproteins in NIDDM. Diabetes 1990; 39: 1017-1027.
33. Griffin BA, Caslake MJ, Yip B, Tait GW, Packard CJ, Shepherd J. Rapid isolation of low density lipoprotein (LDL) subfractions from plasma by density gradient ultracentrifugation. Atherosclerosis 1990; 83: 59-67.
34. Tilly-Kiesi M, Knudsen P, Groop L, Taskinen M-R, the Botnia study group. Hyperinsulinemia and insulin resistance are associated with multiple abnormalities of lipoprotein subclasses in glucose-tolerant relatives of NIDDM patients. J. Lipid Res. 1996; 37: 1569-1578.
35. Georgieva AM, van Greevenbroek MMJ, Krauss RM, Brouwers MCGJ, Vermeulen VMMJ, Robertus-Teunissen MG, van der Kallen CJH, de Bruin TWA. Subclasses of low-density lipoprotein and very low-density lipoprotein in familial combined hyperlipidemia: relationship to multiple lipoprotein phenotype. Arterioscler. Thromb. Vasc. Biol. 2004; 24: 744-749.
36. Öörni K, Posio P, Ala-Korpela M, Jauhiainen M, Kovanen PT. Sphingomyelinase induces aggregation and fusion of small very low-density lipoprotein and intermediate-density lipoprotein particles and increases their retention to human arterial proteoglycans. Arterioscler Thromb. Vasc. Biol. 2005; 25: 1678-1683.
37. Otvos JD. Measurement of lipoprotein subclass profiles by nuclear magnetic resonance spectroscopy. Clin. Lab. 2002; 48: 171-180.
38. Otvos JD, Jeyarajah EJ, Bennett DW, Krauss RM. Development of a proton nuclear magnetic resonance spectroscopic method for determining plasma lipoprotein concentrations and subspecies distributions from a single, rapid measurement. Clin. Chem. 1992; 38: 1632-1638.
39. Otvos J, Jeyarajah E, Bennett D. A spectroscopic approach to lipoprotein subclass analysis. J. Clin. Ligand Assay 1996; 19: 184-189.
40. 1H-NMR-based metabonomics. Nat. Med. 2002; 8: 1439-1444.
41. Kirschenlohr HL, Griffin JL, Clarke SC, Rhydwen R, Grace AA, Schofield PM, Brindle KM, Metcalfe JC. Proton NMR analysis of plasma is a weak predictor of coronary artery disease. Nat. Med. 2006; 12: 705-710.
42. Hannuksela M, Marcel YL, Kesäniemi YA, Savolainen MJ. Reduction in the concentration and activity of plasma cholesteryl ester transfer protein by alcohol. J Lipid Res. 1992; 33: 737-744.
43. Laatikainen R, Niemitz M, Malaisse WJ, Biesemans M, Willem RA. Computational strategy for the deconvolution of NMR spectra with multiplet structures and constraints: analysis of overlapping C-13-H-2 multiplets of C-13 enriched metabolites from cell suspensions incubated in deuterated media. Magn. Reson. Med. 1996; 36: 359-365.
44. Colhoun HM, Otvos JD, Rubens MB, Taskinen MR, Underwood SR, Fuller JH. Lipoprotein subclasses and particle sizes and their relationship with coronary artery calcification in men and women with and without type 1 diabetes. Diabetes 2002; 51: 1949-1956.
45. Jenkins AJ, Lyons TJ, Zheng D, Otvos JD, Lackland DT, McGee D, Garvey WT, Klein RL, The DCCT/EDIC research group. Serum lipoproteins in the diabetes control and complications trial/epidemiology of diabetes intervention and complications cohort. Associations with gender and glycemia. Diabetes Care 2003; 26: 810-818.
46. van Heyningen C. Lipid metabolism: lipoproteins in the metabolic syndrome and subclass sex and age differences. Curr. Opin. Lipidol. 2005; 16: 119-120.
47. Superko HR. Lipoprotein subclasses and atherosclerosis. Front. Biosci. 2001; 6: 355-365.
48. Cottrell M. Theoretical aspects of the som algorithm. Neurocomputing 1998; 21: 119-138.
49. Venna J, Kaski S. Neighborhood preservation in nonlinear projection methods: an experimental study. In Proceedings of International Conference on Artificial Neural Networks (ICANN), Vienna, Austria, 2001.
50. 1H NMR-determined diffusion coefficients to characterize lipoprotein fractions in human blood plasma. Magn. Reson. Chem. 2002; 40: S83-S88.
51. 1H-NMR and chemometrics. In Magnetic Resonance in Food Science, Latest Developments, Webb GA, Belton PS, Gil AM, Rutledge DN (eds). The Royal Society of Chemistry: Cambridge, 2002; 101-109.
52. Petersen M, Dyrby M, Toubro S, Engelsen SB, Nørgaard L, Pedersen HT, Dyerberg J. Quantification of lipoprotein subclasses by proton nuclear magnetic resonance-based partial least-squares regression models. Clin. Chem. 2005; 51: 1457-1461.
53. Dyrby M, Petersen M, Whittaker AK, Lambert L, Nørgaard L, Bro R, Engelsen SB. Analysis of lipoproteins using 2D diffusion-edited NMR spectroscopy and multi-way chemometrics. Anal. Chim. Acta. 2005; 531: 209-216.
54. Nicholson JK, Connelly J, Lindon JC, Holmes E. Metabonomics: a platform for studying drug toxicity and gene function. Nat. Rev. Drug Disc. 2002; 1: 153-161.
55. Griffin JL. Metabolic profiles to define the genome: can we hear the phenotypes? Philos. Trans. R. Soc. Lond. B 2004; 359: 857-871.
56. Bollard ME, Stanley EG, Lindon JC, Nicholson JK, Holmes E. NMR-based metabonomic approaches for evaluating physiological influences on biofluid composition. NMR Biomed. 2005; 18: 143-162.
57. Steinberg D. Atherogenesis in perspective: Hypercholesterolemia and inflammation as partners in crime. Nat. Med. 2002; 8: 1211-1217.
58. Chmurny GN, Hilton BD, Halverson D, McGregor GN, Klose J, Issaq HJ, Muschik GM, Urba WJ, Mellini MI, Costello R, Papadopoulos NM, Caporaso N, Smith ICP, Czuba M, Kroft T, Monck M, Saunders JK, Préfontaine M. An NMR blood test for cancer: a critical assessment. NMR Biomed. 1988; 1: 136-150.
59. Everett CJ, Mainous AG 3rd, Koopman RJ, Diaz VA. Predicting coronary heart disease risk using multiple lipid measures. Am. J. Cardiol. 2005; 95: 986-988.
60. Lounila J, Ala-Korpela M, Jokisaari J, Savolainen MJ, Kesäniemi YA. Effects of orientational order and particle size on the NMR line positions of lipoproteins. Phys. Rev. Lett. 1994; 72: 4049-4052.
61. Murphy HC, Ala-Korpela M, White JJ, Raoof A, Bell JD, Barnard ML, Bums SP, Iles RA. Evidence for distinct behaviour of phosphatidyleholine and sphingomyelin at the low density lipoprotein surface. Biochem. Biophys. Res. Comm. 1997; 234: 733-737.
62. Ala-Korpela M, Lankinen N, Salminen A, Suna T, Soininen P, Laatikainen R, Ingman P, Jauhiainen M, Taskinen MR, Héberger K, Kaski K. The inherent accuracy of 1H NMR spectroscopy to quantify plasma lipoproteins is subclass dependent. Atherosclerosis 2006; in press.
63. Lindon JC, Holmes E, Bollard ME, Stanley EG, Nicholson JK. Metabonomics technologies and their applications in physiological monitoring, drug safety assessment and disease diagnosis. Biomarkers 2004; 9: 1-31.
64. Hoehn F, Lindner E, Mayer HA, Hermle T, Rosenstiel W. Neural networks evaluating NMR data: an approach to visualize similarities and relationships of sol-gel derived inorganic-organic and organometallic hybrid polymers. J. Chem. Inf. Comput. Sci. 2002; 42: 36-45.
65. Mierisovä Š, Ala-Korpela M. MR spectroscopy quantitation: a review of frequency domain methods. NMR Biomed 2001; 14: 247-259.
66. 1H NMR: application in metabonomic toxicology studies. Anal. Chem. 2005; 77: 4556-4562.
67. Ratiney H, Sdika M, Coenradie Y, Cavassila. S, van Ormondt D, Graveron-Demilly D. Time-domain semi-parametric estimation based on a metabolite basis set. NMR Biomed 2005; 18: 1-13.
68. Festa A, Williams K, Hanley AJG, Otvos JD, Goff DC, Wagenknecht LE, Haffner SM. Nuclear magnetic resonance lipoprotein abnormalities in prediabetic subjects in the insulin resistance atherosclerosis study. Circulation 2005; 111: 3465-3472.
69. 1H-nuclear magnetic spectroscopy followed by principal component analysis and hierarchical cluster analysis to demonstrate effects of statins on hyperlipidemic patients. NMR Biomed. 2005; 18: 421-429.