Chemometric strategy for untargeted lipidomics: Biomarker detection and identification in stressed human placental cells

Analytica Chimica Acta

Volumn 854, Issue , 2015, Pages 20-33

  Gorrochategui, Eva ^a   Casas, Josefina ^b   Porte, Cinta ^a   Lacorte, Sílvia ^a   Tauler, Romà ^a  

^a INSTITUTE OF ENVIRONMENTAL ASSESSMENT AND WATER RESEARCH   (Spain)

^b INSTITUTE OF ADVANCED CHEMISTRY OF CATALONIA IQAC CSIC   (Spain)

Author keywords

Biomarkers; Liquid chromatography mass spectrometry; Multivariate curve resolution alternating least squares; Obesogens; Partial least squares discriminant analysis; Untargeted lipidomics

Indexed keywords

BIOMARKERS; CELL CULTURE; CELLS; DISCRIMINANT ANALYSIS; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; IDENTIFICATION (CONTROL SYSTEMS); INDUCTIVELY COUPLED PLASMA; LIPIDS; LIQUIDS; MASS SPECTROMETRY; MATRIX ALGEBRA;

LIPIDOMICS; LIQUID CHROMATOGRAPHY - MASS SPECTROMETRIES; MULTIVARIATE CURVE RESOLUTION-ALTERNATING LEAST SQUARES; OBESOGENS; PARTIAL LEAST SQUARES - DISCRIMINANT ANALYSIS;

LEAST SQUARES APPROXIMATIONS;

BIOLOGICAL MARKER; CHOLESTEROL ESTER; DIACYLGLYCEROL DERIVATIVE; LIPIDOME; LYSOPLASMALOGEN; PERFLUORO COMPOUND; PHOSPHATIDYLCHOLINE; PLASMALOGEN; SPHINGOMYELIN; TRIACYLGLYCEROL; TRIBUTYLTIN; UNCLASSIFIED DRUG; XENOBIOTIC AGENT; LIPID;

ARTICLE; CELL STRESS; CHEMICAL PARAMETERS; CHEMOMETRIC ANALYSIS; CHORIOCARCINOMA CELL LINE; COMPARATIVE STUDY; CONTROLLED STUDY; ELUTION; EXTRACTION; HUMAN; HUMAN CELL; JEG 3 CELL LINE; LIPID ANALYSIS; LIPID DISRUPTION; LIPIDOMICS; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MOLECULAR BIOLOGY; MOLECULAR DYNAMICS; MULTIVARIATE CURVE RESOLUTION ALTERNATING LEAST SQUARES; PARTIAL LEAST SQUARES REGRESSION; PROCESS OPTIMIZATION; REGRESSION ANALYSIS; RETENTION TIME; SOLID LIQUID EXTRACTION; STATISTICAL MODEL; TIME OF FLIGHT MASS SPECTROMETRY; TIME SERIES ANALYSIS; ULTRA PERFORMANCE LIQUID CHROMATOGRAPHY; UNTARGETED LIPIDOMICS; CELL LINE; CYTOLOGY; FEMALE; METABOLISM; PLACENTA; PREGNANCY;

BIOLOGICAL MARKERS; CELL LINE; FEMALE; HUMANS; LIPIDS; PLACENTA; PREGNANCY;

EID: 84919362760     PISSN: 00032670     EISSN: 18734324     Source Type: Journal    
DOI: 10.1016/j.aca.2014.11.010     Document Type: Article

References (50)

1. Oresic M., Hänninen V.A., Vidal-Puig A. Lipidomics: a new window to biomedical frontiers. Trends Biotechnol. 2008, 26:647-652.
2. Van Meer G. Cellular lipidomics. EMBO J. 2005, 24:3159-3165.
3. Shi Y., Burn P. Lipid metabolic enzymes: emerging drug targets for the treatment of obesity. Nat. Rev. Drug Discov. 2004, 3:695-710.
4. Blumberg B. Obesogens, stem cells and the maternal programming of obesity. J. Dev. Orig. Health Dis. 2011, 2:3-8.
5. Stahl T., Mattern D., Brunn H. Toxicology of perfluorinated compounds. Environ. Sci. Eur. 2011, 23-38:1-52.
6. Buhrke T., Kibellus A., Lampen A. In vitro toxicological characterization of perfluorinated carboxylic acids with different carbon chain lengths. Toxicol. Lett. 2013, 218:97-104.
7. Gilliland F.D., Mandel J.S. Serum perfluorooctanoic acid and hepatic enzymes, lipoproteins, and cholesterol: a study of occupationally exposed men. Am. J. Ind. Med. 1996, 29:560-568.
8. Nelson J.W., Hatch E.E., Webster T.F. Exposure to polyfluoroalkyl chemicals and cholesterol, body weight, and insulin resistance in the general U.S. population. Environ. Health Perspect. 2010, 118:197-202.
9. Khalil M.B., Hou W., Zhou H., Elisma F., Swayne L.A., Blanchard A.P., Yao Z., Bennett S.A.L., Figeys D. Lipidomics era: accomplishments and challenges. Mass Spectrom. Rev. 2009, 29:877-929.
10. Piomelli D., Astarita G., Rapaka R. A neuroscientist's guide to lipidomics. Nat. Rev. Neurosci. 2007, 8:743-754.
11. Han X., Gross R.W. Global analyses of cellular lipidomes directly from crude extracts of biological samples by ESI mass spectrometry: a bridge to lipidomics. J. Lipid. Res. 2003, 44:1071-1079.
12. Spener F., Lagarde M., Géloen A., Record M. Editorial: what is lipidomics?. Eur. J. Lipid Sci. Technol. 2003, 105:481-482.
13. Castro-Perez J.M., Kamphorst J., Degroot J., Lafeber F., Goshawk J., Yu K., Shockor J.P., Vreeken R.J., Hankemeier T. Comprehensive LC-MSE lipidomic analysis using a shotgun approach and its application to biomarker detection and identification in osteoarthritis patients. J. Proteome Res. 2010, 9:2377-2389.
14. Yetukuri L., Katajamaa M., Medina-Gomez G., Seppänen-Laakso T., Vidal-Puig A., Oresic M. Bioinformatics strategies for lipidomics analysis: characterization of obesity related hepatic steatosis. BMC Syst. Biol. 2007, 1:12.
15. Chadeau-Hyam M., Campanella G., Jombart T., Bottolo L., Portengen L., Vineis P., Liquet B., Vermeulen R.C.H. Deciphering the complex: methodological overview of statistical models to derive OMICS-based biomarkers. Environ. Mol. Mutagen. 2013, 54:542-557.
16. Boccard J., Rutledge D.N. A consensus orthogonal partial least squares discriminant analysis (OPLS-DA) strategy for multiblock Omics data fusion. Anal. Chim. Acta 2013, 769:30-39.
17. Farrés M., Piña B., Tauler R. Chemometric evaluation of Saccharomyces cerevisiae metabolic profiles using LC-MS. Metabolomics 2014, 10.1007/s11306-014-0689-z.
18. Siano G.G., Sánchez Pérez I., Gil García M.D., Martínez Galera M., Goicochea H.C. Multivariate curve resolution modeling of liquid chromatography-mass spectrometry data in a comparative study of the different endogenous metabolites behaviour in two tomato cultivars treated with carbofuran pesticide. Talanta 2011, 85:264-275.
19. Tauler R. Multivariate curve resolution applied to second order data. Chemom. Intell. Lab. Syst. 1995, 30:133-146.
20. de Juan A., Tauler R. Factor analysis of hyphenated chromatographic data. Exploration, resolution and quantification of multicomponent systems. J. Chromatogr. A 2007, 1158:184-195.
21. Barker M., Rayens W.S. Partial least squares for discrimination. J. Chemom. 2003, 17:166-173.
22. Wold S., Sjöström M., Eriksson L. PLS-regression: a basic tool of chemometrics. Chemom. Intell. Lab. Syst. 2001, 58:109-130.
23. Hochberg Y., Tamhane A.C. Multiple Comparison Procedures 1987, John Wiley & Sons, Hoboken, NJ.
24. Godfrey K. Comparing the means of several groups. N. Engl. J. Med. 1985, 311:1450-1456.
25. Tukey J.W. Some thoughts on clinical trials, especially problems of multiplicity. Science 1977, 198:679-684.
26. Box G.E.P., Hunter W.G., Stuart Hunter J. Statistics for Experimenters: An Introduction to Design, Data Analysis, and Model Building 1978, John Wiley & Sons.
27. Peña Sánchez de Rivera D. Estadística. Modelos y métodos. 2. Modelos lineales y series temporales 1989, Alianza Universidad Textos.
28. Gorrochategui E., Pérez-Albaladejo E., Casas J., Lacorte S., Porte C. Perfluorinated chemicals: differential toxicity, inhibition of aromatase activity and alteration of cellular lipids in human placental cells. Toxicol. Appl. Pharmacol. 2014, 277:124-130.
29. Gorrochategui E., Casas J., Pérez-Albaladejo E., Jáuregui O., Porte C., Lacorte S. Characterization of complex lipid mixtures in contaminant exposed JEG-3 cells using liquid chromatography and high-resolution mass spectrometry. Environ. Sci. Pollut. Res. 2014, 10.1007/s11356-014-3172-5.
30. Olsen G.W., Gilliland F.D., Burlew M.M., Burris J.M., Mandel J.S., Mandel J.H. An epidemologic investigation of reproductive hormones in men with occupational exposure to perfluorooctanoic acid. J. Occup. Environ. Med. 1998, 40:614-622.
31. Christie W.W. Rapid separation and quantification of lipid classes by high-performance liquid chromatography and mass (light-scattering) detection. J. Lipid Res. 1985, 26:507-512.
32. Garanto A., Mandal N.A., Egido-Gabás M., Marfany G., Fabriàs G., Anderson R.E., Casas J., González-Duarte R. Specific sphingolipid content decrease in Cerkl knockdown mouse retinas. Exp. Eye Res. 2013, 110:96-106.
33. Jaumot J., Gargallo R., de Juan A., Tauler R. A graphical user-friendly interface for MCR-ALS: a new tool for multivariate curve resolution in MATLAB. Chemom. Intell. Lab. Syst. 2005, 6:101-110.
34. Golub G., Solna K., Van Dooren P. Computing the SVD of a general matrix product/quotient. SIAM J. Matrix Anal. Appl. 2000, 22:1-19.
35. Bu D., Brown C.W. Self-modeling mixture analysis by interactive principal component analysis. Appl. Spectrosc. 2000, 54:1214-1221.
36. Tauler R., Barceló D. Multivariate curve resolution applied to liquid chromatography-diode array detection. Trends Anal. Chem. 1993, 12:319-327.
37. Tauler R., Smilde A., Kowalski B. Selectivity local rank, three-way data analysis and ambiguity in multivariate curve resolution. J. Chemom. 1995, 9:31-58.
38. PLS-Partial Least Squares Projections to Latent Structures 1993, ESCOM Science Publishers, Leiden. S. Wold, A. Johansson, M. Cochi (Eds.).
39. Wold S. PLS for multivariate linear modeling. QSAR: Chemometric Methods in Molecular Design, Methods and Principles in Medicinal Chemistry 1995, vol. 2:195-218. Verlag Chemie, Weinheim.
40. Chong I.-G., Jun C.-H. Performance of some variable selection methods when multicollinearity is present. Chemom. Intell. Lab. Syst. 2005, 78:103-112.
41. Rajalahti T., Arneberg R., Kroksveen A.C., Berle M., Myhr K.-M., Kvalheim O.M. Discriminating variable test and selectivity ratio plot: quantitative tools for interpretation and variable (biomarker) selection in complex spectral or chromatographic profiles. Anal. Chem. 2009, 81:2581-2590.
42. Andersen C.M., Bro R. Variable selection in regression-a tutorial. J. Chemom. 2010, 24:728-737.
43. Janer G., Navarro J.C., Porte C. Exposure to TBT increases accumulation of lipids and alters fatty acid homeostasis in the ramshorn snail Marisa cornuarietis. Comp. Biochem. Physiol. C 2007, 146:368-374.
44. Grün F., Blumberg B. Environmental obesogens: organotins and endocrine disruption via nuclear receptor signaling. Endocrinology 2006, 147:S50-S55.
45. Pereira-Fernandes A., Vanparys C., Hectors T.L.M., Vergauwen L., Knapen D., Jorens P.G., Blust R. Unraveling the mode of action of an obesogen: mechanistic analysis of the model obesogen tributyltin in the 3T3-L1 cell line. Mol. Cell. Endocrinol. 2013, 370:52-64.
46. Xie W., Ludewig G., Wang K., Lehmler H.J. Model and cell membrane partitioning of perfluorooctanesulfonate is independent of the lipid chain length. Colloids Surf. B 2010, 76:128-136.
47. Xie W., Bothun G.D., Lehmler H.J. Partitioning of perfluorooctanoate into phosphatidylcholine bilayers is chain length-independent. Chem. Phys. Lipids 2010, 163:300-308.
48. Higdon A., Diers A.R., Oh J.Y., Landar A., Darley-Usmar V.M. Cell signaling by reactive lipid species: new concepts and molecular mechanisms. Biochem. J. 2012, 442:453-464.
49. Engelmann B., Brautigam C., Thiery J. Plasmalogen phospholipids as potential protectors against lipid-peroxidation of low-density lipoproteins. Biochem. Biophys. Res. Commun. 1994, 204:1235-1242.
50. Engelman B. Plasmalogens: targets for oxidants and major lipophilic antioxidants. Biochem. Soc. Trans. 2004, 32:147-150.