Development of an optimized protocol for NMR metabolomics studies of human colon cancer cell lines and first insight from testing of the protocol using DNA G-quadruplex ligands as novel anti-cancer drugs

Metabolites

Volumn 6, Issue 1, 2016, Pages

  Lauri, Ilaria ^a   Savorani, Francesco ^b,c   Iaccarino, Nunzia ^a   Zizza, Pasquale ^d   Pavone, Luigi Michele ^a   Novellino, Ettore ^a   Engelsen, Søren Balling ^b   Randazzo, Antonio ^a  

^a UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c POLITECNICO DI TORINO   (Italy)

^d REGINA ELENA NATIONAL CANCER INSTITUTE   (Italy)

Author keywords

Cell metabolomics; Colon cancer; G quadruplex ligands; Multivariate statistical analysis; NMR spectroscopy

Indexed keywords

ANTINEOPLASTIC AGENT; GUANINE QUADRUPLEX;

ARTICLE; COLON CANCER; CONTROLLED STUDY; HUMAN; HUMAN CELL; IC50; LIQUID CHROMATOGRAPHY; MASS FRAGMENTOGRAPHY; METABOLOMICS; NUCLEAR MAGNETIC RESONANCE IMAGING; PRINCIPAL COMPONENT ANALYSIS; PROTON NUCLEAR MAGNETIC RESONANCE; REPRODUCIBILITY;

EID: 85006205290     PISSN: None     EISSN: 22181989     Source Type: Journal    
DOI: 10.3390/metabo6010004     Document Type: Article

References (41)

1. Griffin, J. Metabonomics: NMR spectroscopy and pattern recognition analysis of body fluids and tissues for characterisation of xenobiotic toxicity and disease diagnosis. Curr. Opin. Chem. Biol. 2003, 7, 648-654. [CrossRef] [PubMed]
2. Andrew Clayton, T.; Lindon, J.C.; Cloarec, O.; Antti, H.; Charuel, C.; Hanton, G.; Provost, J.-P.; Le Net, J.-L.; Baker, D.; Walley, R.J.; et al. Pharmaco-metabonomic phenotyping and personalized drug treatment. Nature 2006, 440, 1073-1077. [CrossRef] [PubMed]
3. Robertson, D.G. Metabonomics in Toxicology: A Review. Toxicol. Sci. 2005, 85, 809-822. [CrossRef] [PubMed]
4. Savorani, F.; Rasmussen, M.A.; Mikkelsen, M.S.; Engelsen, S.B. A primer to nutritional metabolomics by NMR spectroscopy and chemometrics. Food Res. Int. 2013, 54, 1131-1145. [CrossRef]
5. Tang, J. Microbial Metabolomics. Curr. Genom. 2011, 12, 391-403. [CrossRef] [PubMed]
6. Cuperlović-Culf, M.; Barnett, D.A.; Culf, A.S.; Chute, I. Cell culture metabolomics: Applications and future directions. Drug Discov. Today 2010, 15, 610-621. [CrossRef] [PubMed]
7. Zhang, A.; Sun, H.; Xu, H.; Qiu, S.; Wang, X. Cell Metabolomics. OMICS 2013, 17, 495-501. [CrossRef] [PubMed]
8. Bai, J.; Wang, M.X.; Chowbay, B.; Ching, C.B.; Chen, W.N. Metabolic profiling of HepG2 cells incubated with S(_) and R(+) enantiomers of anti-coagulating drug warfarin. Metabolomics 2011, 7, 353-362. [CrossRef] [PubMed]
9. Panopoulos, A.D.; Yanes, O.; Ruiz, S.; Kida, Y.S.; Diep, D.; Tautenhahn, R.; Herrerías, A.; Batchelder, E.M.; Plongthongkum, N.; Lutz, M.; et al. The metabolome of induced pluripotent stem cells reveals metabolic changes occurring in somatic cell reprogramming. Cell. Res. 2012, 22, 168-177. [CrossRef] [PubMed]
10. Serkova, N.; Glunde, K. Metabolomics of Cancer. In Tumor Biomarker Discovery SE -20; Tainsky, M.A., Ed.; Methods in Molecular Biology; Humana Press: New York, NY, USA, 2009; Volume 520, pp. 273-295.
11. Jemal, A.; Bray, F.; Center, M.M.; Ferlay, J.;Ward, E.; Forman, D. Global cancer statistics. CA Cancer J. Clin. 2011, 61, 69-90. [CrossRef] [PubMed]
12. Frezza, C.; Zheng, L.; Tennant, D.A.; Papkovsky, D.B.; Hedley, B.A.; Kalna, G.; Watson, D.G.; Gottlieb, E. Metabolic profiling of hypoxic cells revealed a catabolic signature required for cell survival. PLoS ONE 2011. [CrossRef] [PubMed]
13. Kotze, H.L.; Armitage, E.G.; Sharkey, K.J.; Allwood, J.W.; Dunn, W.B.; Williams, K.J.; Goodacre, R. A novel untargeted metabolomics correlation-based network analysis incorporating human metabolic reconstructions. BMC Syst. Biol. 2013, 7, 107. [CrossRef] [PubMed]
14. Loftus, N.J.; Lai, L.; Wilkinson, R.W.; Odedra, R.; Wilson, I.D.; Barnes, A.J. Global Metabolite Profiling of Human Colorectal Cancer Xenografts in Mice Using HPLC-MS/MS. J. Proteome Res. 2013, 12, 2980-2986. [CrossRef] [PubMed]
15. Tolstikov, V.; Nikolayev, A.; Dong, S.; Zhao, G.; Kuo, M.-S. Metabolomics analysis of metabolic effects of nicotinamide phosphoribosyltransferase (NAMPT) inhibition on human cancer cells. PLoS ONE 2014. [CrossRef] [PubMed]
16. Aftab, O.; Engskog, M.K.R.; Haglöf, J.; Elmsjö, A.; Arvidsson, T.; Pettersson, C.; Hammerling, U.; Gustafsson, M.G. NMR Spectroscopy-Based Metabolic Profiling of Drug-Induced Changes in Vitro Can Discriminate between Pharmacological Classes. J. Chem. Inf. Model. 2014, 54, 3251-3258. [CrossRef] [PubMed]
17. Balasubramanian, S.; Neidle, S. G-quadruplex nucleic acids as therapeutic targets. Curr. Opin. Chem. Biol. 2009, 13, 345-353. [CrossRef] [PubMed]
18. Brooks, T.A.; Kendrick, S.; Hurley, L. Making sense of G-quadruplex and i-motif functions in oncogene promoters. FEBS J. 2010, 277, 3459-3469. [CrossRef] [PubMed]
19. Biffi, G.; Tannahill, D.; McCafferty, J.; Balasubramanian, S. Quantitative Visualization of DNA G-quadruplex Structures in Human Cells. Nat. Chem. 2013, 5, 182-186. [CrossRef] [PubMed]
20. Bidzinska, J.; Cimino-Reale, G.; Zaffaroni, N.; Folini, M. G-quadruplex structures in the human genome as novel therapeutic targets. Molecules 2013, 18, 12368-12395. [CrossRef] [PubMed]
21. Cosconati, S.; Rizzo, A.; Trotta, R.; Pagano, B.; Iachettini, S.; de Tito, S.; Lauri, I.; Fotticchia, I.; Giustiniano, M.; Marinelli, L.; et al. Shooting for Selective Druglike G-Quadruplex Binders: Evidence for Telomeric DNA Damage and Tumor Cell Death. J. Med. Chem. 2012, 55, 9785-9792. [CrossRef] [PubMed]
22. Read, M.; Harrison, R.J.; Romagnoli, B.; Tanious, F.A.; Gowan, S.H.; Reszka, A.P.;Wilson,W.D.; Kelland, L.R.; Neidle, S. Structure-based design of selective and potent G quadruplex-mediated telomerase inhibitors. Proc. Natl. Acad. Sci. USA 2001, 98, 4844-4849. [CrossRef] [PubMed]
23. Di Leva, F.S.; Zizza, P.; Cingolani, C.; D'Angelo, C.; Pagano, B.; Amato, J.; Salvati, E.; Sissi, C.; Pinato, O.; Marinelli, L.; et al. Exploring the Chemical Space of G-Quadruplex Binders: Discovery of a Novel Chemotype Targeting the Human Telomeric Sequence. J. Med. Chem. 2013, 56, 9646-9654. [CrossRef] [PubMed]
24. Leonetti, C.; Amodei, S.; D'Angelo, C.; Rizzo, A.; Benassi, B.; Antonelli, A.; Elli, R.; Stevens, M.F.G.; D'Incalci, M.; Zupi, G.; et al. Biological Activity of the G-Quadruplex Ligand RHPS4 (3,11-Difluoro-6,8,13-trimethyl-8H-quino[4,3,2-kl]acridinium methosulfate) Is Associated with Telomere Capping Alteration. Mol. Pharmacol. 2004, 66, 1138-1146. [CrossRef] [PubMed]
25. Young, R.C.; Ozols, R.F.; Myers, C.E. The Anthracycline Antineoplastic Drugs. N. Engl. J. Med. 1981, 305, 139-153. [CrossRef] [PubMed]
26. Salvati, E.; Leonetti, C.; Rizzo, A.; Scarsella, M.; Mottolese, M.; Galati, R.; Sperduti, I.; Stevens, M.F.G.; D'Incalci, M.; Blasco, M.; et al. Telomere damage induced by the G-quadruplex ligand RHPS4 has an antitumor effect. J. Clin. Investig. 2007, 117, 3236-3247. [CrossRef] [PubMed]
27. Bligh, E.G.; Dyer,W.J. A rapid method of total lipid extraction and purification. Can. J. Biochem. Physiol. 1959, 37, 911-917. [CrossRef] [PubMed]
28. Savorani, F.; Tomasi, G.; Engelsen, S.B. icoshift: A versatile tool for the rapid alignment of 1D NMR spectra. J. Magn. Reson. 2010, 202, 190-202. [CrossRef] [PubMed]
29. Eriksson, L.; Johansson, E.; Kettaneh-Wold, N.;Wold, S. Introduction to Multi- and Megavariate Data Anaysis Using Projection Methods (PCA & PLS); Umetrics: Umeå, Sweden, 1999.
30. Hotelling, H. Analysis of a complex of statistical variables into principal components. J. Educ. Psychol. 1933, 24, 417-441. [CrossRef]
31. Martens, H.A.; Dardenne, P. Validation and verification of regression in small data sets. Chemom. Intell. Lab. Syst. 1998, 44, 99-121. [CrossRef]
32. Wishart, D.S.; Jewison, T.; Guo, A.C.; Wilson, M.; Knox, C.; Liu, Y.; Djoumbou, Y.; Mandal, R.; Aziat, F.; Dong, E.; et al. HMDB 3.0-The Human Metabolome Database in 2013. Nucleic Acids Res. 2013, 41, D801-D807. [CrossRef] [PubMed]
33. Bertini, I.; Hu, X.; Luchinat, C. Global metabolomics characterization of bacteria: Pre-analytical treatments and profiling. Metabolomics 2014, 10, 241-249. [CrossRef]
34. Duarte, I.F.; Marques, J.; Ladeirinha, A.F.; Rocha, C.; Lamego, I.; Calheiros, R.; Silva, T.M.; Marques, M.P.M.; Melo, J.B.; Carreira, I.M.; et al. Analytical Approaches toward Successful Human Cell Metabolome Studies by NMR Spectroscopy. Anal. Chem. 2009, 81, 5023-5032. [CrossRef] [PubMed]
35. Wang, X.; Hu, M.; Feng, J.; Liu, M.; Hu, J. 1H NMR metabolomics study of metastatic melanoma in C57BL/6J mouse spleen. Metabolomics 2014, 10, 1129-1144. [CrossRef] [PubMed]
36. Cloarec, O.; Dumas, M.-E.; Craig, A.; Barton, R.H.; Trygg, J.; Hudson, J.; Blancher, C.; Gauguier, D.; Lindon, J.C.; Holmes, E.; et al. Statistical Total Correlation Spectroscopy: An Exploratory Approach for Latent Biomarker Identification from Metabolic 1H NMR Data Sets. Anal. Chem. 2005, 77, 1282-1289. [CrossRef] [PubMed]
37. Xia, J.; Psychogios, N.; Young, N.; Wishart, D.S. MetaboAnalyst: A web server for metabolomic data analysis and interpretation. Nucleic Acids Res. 2009, 37, W652-W660. [CrossRef] [PubMed]
38. Martineau, E.; Tea, I.; Loaëc, G.; Giraudeau, P.; Akoka, S. Strategy for choosing extraction procedures for NMR-based metabolomic analysis of mammalian cells. Anal. Bioanal. Chem. 2011, 401, 2133-2142. [CrossRef] [PubMed]
39. Wenzel, U.; Schoberl, K.; Lohner, K.; Daniel, H. Activation of mitochondrial lactate uptake by flavone induces apoptosis in human colon cancer cells. J. Cell. Physiol. 2005, 202, 379-390. [CrossRef] [PubMed]
40. Cao, B.; Li, M.; Zha, W.; Zhao, Q.; Gu, R.; Liu, L.; Shi, J.; Zhou, J.; Zhou, F.; Wu, X.; et al. Metabolomic approach to evaluating adriamycin pharmacodynamics and resistance in breast cancer cells. Metabolomics 2013, 9, 960-973. [CrossRef] [PubMed]
41. Krishnan, P.; Kruger, N.J.; Ratcliffe, R.G. Metabolic fingerprinting and profiling in plants using NMR. J. Exp. Bot. 2005, 56, 255-265. [CrossRef] [PubMed]