Metabolomics in cell culture - A strategy to study crucial metabolic pathways in cancer development and the response to treatment

Archives of Biochemistry and Biophysics

Volumn 564, Issue , 2014, Pages 100-109

  Halama, Anna ^a  

^a WEILL CORNELL MEDICAL COLLEGE   (Qatar)

Author keywords

Cancer cell lines; Cell culture; Drug screening; Metabolic alterations; Metabolomics

Indexed keywords

ANTINEOPLASTIC AGENT; BIOLOGICAL MARKER;

APOPTOSIS; BREAST CANCER CELL LINE; CANCER CELL; CANCER CELL CULTURE; CANCER GROWTH; COLORECTAL CANCER CELL LINE; DRUG DEVELOPMENT; DRUG RESPONSE; DRUG SCREENING; GAS CHROMATOGRAPHY; GAS LIQUID CHROMATOGRAPHY; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HIGH THROUGHPUT SCREENING; HUMAN; LIQUID CHROMATOGRAPHY; METABOLOMICS; NONHUMAN; OVARIAN CANCER CELL LINE; PANCREATIC CANCER CELL LINE; PROSTATE CANCER CELL LINE; REVIEW; TREATMENT OUTCOME; TREATMENT RESPONSE; ULTRA PERFORMANCE LIQUID CHROMATOGRAPHY; ANIMAL; METABOLISM; METABOLOME; NEOPLASMS; PROCEDURES; TUMOR CELL LINE;

ANIMALS; BIOLOGICAL MARKERS; CELL LINE, TUMOR; DRUG SCREENING ASSAYS, ANTITUMOR; HUMANS; METABOLOME; METABOLOMICS; NEOPLASMS;

EID: 84908341419     PISSN: 00039861     EISSN: 10960384     Source Type: Journal    
DOI: 10.1016/j.abb.2014.09.002     Document Type: Review

References (156)

1. S.G. Oliver Trends Biotechnol. 16 9 1998 373 378
2. J. Adamski Genome Med. 4 4 2012 1 7
3. J.K. Nicholson, J.C. Lindon, and E. Holmes Xenobiotica 29 11 1999 1181 1189
4. O. Fiehn Nat. Biotechnol. 18 11 2000 1157 1161
5. L. Pauling Proc. Natl. Acad. Sci. U.S.A. 68 10 1971 2374 2376
6. E.M. Lenz, and I.D. Wilson J. Proteome Res. 6 2 2007 443 458
7. W.B. Dunn, and D.I. Ellis TrAC Trends Anal. Chem. 24 4 2005 285 294
8. M.R. Wenk Nat. Rev. Drug Discov. 4 7 2005 594 610
9. W.J. Griffiths, and Y. Wang Chem. Soc. Rev. 38 7 2009 1882 1896
10. J. Esko, N. Sharon, Essentials of Glycobiology, in: A. Varki, 2009, pp. 321-333.
11. N. Fujitani Proc. Natl. Acad. Sci. 110 6 2013 2105 2110
12. U. Ceglarek J. Steroid Biochem. Mol. Biol. 121 3-5 2010 479 480
13. A. Artati, et al., Assay tools for metabolomics, in: K. Suhre (Ed.), Genetics Meets Metabolomics, Springer, New York, 2012, pp. 13-38.
14. M. Katajamaa, J. Miettinen, and M. Orešič Bioinformatics 22 5 2006 634 636
15. J. Xia BMC Bioinformatics 9 1 2008 507
16. F. Fernández-Albert, et al., An R package to analyse LC/MS metabolomic data: MAIT (Metabolite Automatic Identification Toolkit). Bioinformatics (2014) btu136.
17. K. Suhre, and P. Schmitt-Kopplin Nucleic Acids Res. 36 Suppl. 2 2008 W481 W484
18. J. Xia Nucleic Acids Res. 37 Suppl. 2 2009 W652 W660
19. G. Kastenmüller, et al., metaP-server: a web-based metabolomics data analysis tool. J. Biomed. Biotechnol. 2011 (2010).
20. M. Kanehisa Nucleic Acids Res. 38 Suppl. 1 2010 D355 D360
21. M. Sud Nucleic Acids Res. 35 Suppl. 1 2007 D527 D532
22. Y. Wang Nucleic Acids Res. 37 Suppl. 2 2009 W623 W633
23. D.S. Wishart Nucleic Acids Res. 37 Suppl. 1 2009 D603 D610
24. S.C. Booth, A. Weljie, and R.J. Turner Comput. Struct. Biotechnol. J. 2013 4
25. J. Krumsiek BMC Syst. Biol. 5 2011 21
26. C. Gieger PLoS Genet. 4 11 2008 e1000282
27. J. Krumsiek PLoS Genet. 8 10 2012 e1003005
28. L.J. Lesko, and A.J. Atkinson Jr. Annu. Rev. Pharmacol. Toxicol. 41 2001 347 366
29. S.A. Ritchie BMC Med. 8 1 2010 13
30. Y. Qiu J. Proteome Res. 8 10 2009 4844 4850
31. A.B. Leichtle Metabolomics 8 4 2012 643 653
32. B. Sitter NMR Biomed. 19 1 2006 30 40
33. B. Sitter NMR Biomed. 23 4 2010 424 431
34. W. Lv, and T. Yang Clin. Biochem. 45 1 2012 127 133
35. H. Zhang Electrophoresis 32 3-4 2011 340 347
36. S. Nishiumi Metabolomics 6 4 2010 518 528
37. D. OuYang Appl. Biochem. Biotechnol. 165 1 2011 148 154
38. A.D. Patterson Cancer Res. 71 21 2011 6590 6600
39. H.W. Ressom Anal. Chim. Acta 743 2012 90 100
40. T. Zhang Clin. Chim. Acta 413 9 2012 861 868
41. C. Denkert Cancer Res. 66 22 2006 10795 10804
42. K. Odunsi Int. J. Cancer 113 5 2005 782 788
43. K.W. Jordan, L.L. Cheng, Expert. Rev. Proteom. 4 (2007) 389-400.
44. A. Sreekumar Nature 457 7231 2009 910 914
45. S. Hori Lung Cancer 74 2 2011 284 292
46. J. Carrola J. Proteome Res. 10 1 2010 221 230
47. A. Nordström, and R. Lewensohn J. Neuroimmune Pharmacol. 5 1 2010 4 17
48. R.G. Harrison Anatom. Rec. 1 5 1907 116 128
49. W.R. Earle J. Natl. Cancer Inst. 4 165212 1943 122 137
50. G. Gey, W. Coffman, M.T. Kubicek, Tissue culture studies of the proliferative capacity of cervical carcinoma and normal epithelium, in: Cancer Research, Am. Assoc. Cancer Research, PO Box 11806, Birmingham, AL 35202, 1952.
51. W.I. Schaeffer In Vitro 20 1 1984 19 24
52. J.R. Masters Nat. Rev. Cancer 2 4 2002 315 319
53. M. Cuperlovic-Culf Drug Discov. Today 15 15-16 2010 610 621
54. Z. León Electrophoresis 34 19 2013 2762 2775
55. M. Volmer, et al., A method for metabolomic sampling of suspended animal cells using fast filtration, in: BMC Proceedings, BioMed Central Ltd., 2011.
56. C.A. Sellick Anal. Chem. 81 1 2008 174 183
57. S. Dietmair Anal. Biochem. 404 2 2010 155 164
58. Q. Teng Metabolomics 5 2 2009 199 208
59. U. Batista Cell Biol. Int. 34 6 2010 663 668
60. K. Dettmer Anal. Bioanal. Chem. 399 3 2011 1127 1139
61. L.P. Silva Anal. Chem. 85 20 2013 9536 9542
62. O. Warburg, F. Wind, and E. Negelein J. Gene. Physiol. 8 6 1927 519 530
63. S.R. Wagle, H.P. Morris, and G. Weber Cancer Res. 23 1963 1003 1007
64. Z. Kovacevic, and H.P. Morris Cancer Res. 32 2 1972 326 333
65. R.J. DeBerardinis Proc. Natl. Acad. Sci. U.S.A. 104 49 2007 19345 19350
66. C. DeSantis CA Cancer J. Clin. 64 1 2014 52 62
67. M. Nair, S. Sandhu, A. Sharma, Curr. Cancer Drug Targets (2014).
68. V.M. Asiago Cancer Res. 70 21 2010 8309 8318
69. C.M. Slupsky Clin. Cancer Res. 16 23 2010 5835 5841
70. M.L. Dória Breast Cancer Res. Treat. 133 2 2012 635 648
71. D. Bullinger BMC Biochem. 8 1 2007 25
72. S. Yamashita, J. Yamashita, and M. Ogawa Br. J. Cancer 69 6 1994 1166 1170
73. I.S. Babina, et al., Semin. Cell Dev. Biol. (2011), PMID: 9599410.
74. X. Zhang, P.W. Majerus, Phosphatidylinositol signalling reactions, in: Seminars in Cell & Developmental Biology, Elsevier, 1998.
75. J.A. Engelman, J. Luo, and L.C. Cantley Nat. Rev. Genet. 7 8 2006 606 619
76. J. Baselga Oncologist 16 Suppl. 1 2011 12 19
77. R. Beger Metabolites 3 3 2013 552 574
78. W. Struck Anal. Bioanal. Chem. 401 7 2011 2039 2050
79. A.J. Sasco Cancer Lett. 108 2 1996 157 162
80. Y.F. Zheng Clin. Biochem. 38 1 2005 24 30
81. K.E. Cano, Y.-J. Li, and Y. Chen J. Proteome Res. 9 10 2010 5382 5388
82. L.S. Vermeer J. Proteome Res. 11 5 2012 2996 3003
83. Z. Shi Cancer Lett. 344 1 2014 47 53
84. A.M. Weljie J. Biomol. NMR 49 3-4 2011 185 193
85. D. Hanahan, and R.A. Weinberg Cell 144 5 2011 646 674
86. X. Zhao, and G. Blobel Proc. Natl. Acad. Sci. U.S.A. 102 13 2005 4777 4782
87. A. Müller Nature 410 6824 2001 50 56
88. R. Siegel, C. DeSantis, and A. Jemal CA Cancer J. Clin. 64 2 2014 104 117
89. C. Ludwig Magn. Reson. Chem. 47 S1 2009 S68 S73
90. Y. Cheng J. Proteome Res. 11 2 2011 1354 1363
91. C. Denkert Mol. Cancer 7 1 2008 72
92. Y. Qiu Clin. Cancer Res. 20 8 2014 2136 2146
93. D. Zimmermann Metabolomics 3 1 2007 13 17
94. G. Alcarraz-Vizán, et al., Biochim. Biophys. Acta - Gene. Subj. (2013).
95. Vander Heiden Science 324 5930 2009 1029 1033
96. J. Boren J. Biol. Chem. 278 31 2003 28395 28402
97. O.C. Velazquez, H.M. Lederer, and J.L. Rombeau Dig Dis Sci 41 4 1996 727 739
98. A. Hague Int. J. Cancer 55 3 1993 498 505
99. T.L. Miller, and M.J. Wolin Appl. Environ. Microbiol. 62 5 1996 1589 1592
100. K. Soergel Clin. Invest. 72 10 1994 742 748
101. R. Siegel CA Cancer J. Clin. 64 1 2014 9 29
102. I.M. Di Gangi, et al., TrAC Trends Analyt. Chem. (2014).
103. O.F. Bathe Cancer Epidemiol. Biomark. Prev. 20 1 2011 140 147
104. R.D. Beger Metabolomics 2 3 2006 125 134
105. M. Watanabe J. Mol. Biomark. Diagn. 3 2012 2
106. J.E. Vance, and G. Tasseva Biochim. Biophys. Acta 1831 3 2013 543 554
107. Y. Fujimura Pancreas 43 2 2014 311 318
108. M.J. Moore J. Clin. Oncol. 25 15 2007 1960 1966
109. M. Wyss, and R. Kaddurah-Daouk Physiol. Rev. 80 3 2000 1107 1213
110. M.M. Robinson Biochem. J. 406 3 2007 407 414
111. M.J. Seltzer Cancer Res. 70 22 2010 8981 8987
112. G. Bergnes Oncol. Res. 8 3 1996 121 130
113. D. Jelovac, and D.K. Armstrong CA Cancer J. Clin. 61 3 2011 183 203
114. M. Basu J. Biol. Chem. 289 3 2014 1415 1428
115. L. Yang, et al., Mol. Syst. Biol. 10(5) (2014).
116. E. Garcia J. Proteome Res. 10 4 2011 1765 1771
117. E.A. Boss NMR Biomed. 13 5 2000 297 305
118. E. Iorio Cancer Res. 65 20 2005 9369 9376
119. D.E. Levy, and C.-K. Lee J. Clin. Invest. 109 9 2002 1143 1148
120. L. Berlicki Mini Rev. Med. Chem. 8 9 2008 869 878
121. O. Teahan Int. J. Biochem. Cell Biol. 43 7 2011 1002 1009
122. T.A. Averna J. Urol. 173 2 2005 433 438
123. M.M. Webber Prostate 47 1 2001 1 13
124. N. Putluri PLoS One 6 7 2011 e21417
125. D.G. Watson Cell. Signal. 25 4 2013 1011 1017
126. A. Dayon PLoS One 4 11 2009 e8048
127. N.J. Pyne, and S. Pyne Nat. Rev. Cancer 10 7 2010 489 503
128. B. Lu PLoS One 6 12 2010 e28837-e28837
129. M.S. Arredouani Clin. Cancer Res. 15 18 2009 5794 5802
130. W.B. Parker Chem. Rev. 109 7 2009 2880 2893
131. C.R. Chong, and D.J. Sullivan Nature 448 2007 645 646
132. Food and Drug Administration, Innovation or stagnation: challenge and opportunity on the critical path to new medical products. Food and Drug Administration, critical path report, 2004.
133. V.C. Abraham, D. Taylor, and J.R. Haskins Trends Biotechnol. 22 1 2004 15 22
134. S. Tiziani Nat. Commun. 2 2011 545
135. S. Tiziani PLoS One 4 1 2009 e4251
136. Y. Abramov Oncol. Res. Featur. Preclin. Clin. Cancer Therap. 20 11 2013 529 536
137. A. Halama J. Intern. Med. 274 5 2013 425 439
138. A. Halama, G. Moller, and J. Adamski OMICS 15 5 2011 325 335
139. G. Rainaldi Radiat. Res. 169 2 2008 170 180
140. L. Mirbahai, et al., Int. J. Biochem. Cell Biol. (2010).
141. M. Watson Mol. Cell. Biol. 29 21 2009 5872 5888
142. Y. Xiao, et al., Neoplasia (New York, NY) 15(10) (2013) 1151.
143. Y. Wang PLoS One 8 5 2013 e63572
144. A. Kamb, S. Wee, and C. Lengauer Nat. Rev. Drug Discov. 6 2 2006 115 120
145. L. Mirbahai NMR Biomed. 25 11 2012 1253 1262
146. S.Y. Proskuryakov, A.G. Konoplyannikov, and V.L. Gabai Exp. Cell Res. 283 1 2003 1 16
147. D.H. Chace, T.A. Kalas, and E.W. Naylor Clin. Chem. 49 11 2003 1797 1817
148. U. Warskulat Arch. Biochem. Biophys. 462 2 2007 202 209
149. T. Takatani Am. J. Physiol. Cell Physiol. 287 4 2004 C949 C953
150. G. Cholewinski, K. Dzierzbicka, and A.M. Kolodziejczyk Pharmacol. Rep. 63 2011 305 336
151. P.-J.V. Hjarnaa Cancer Res. 59 22 1999 5751 5757
152. A. Ertel Mol. Cancer 5 1 2006 55
153. W.D. Stein Cancer Res. 64 8 2004 2805 2816
154. R. Sandberg, and I. Ernberg Proc. Natl. Acad. Sci. U.S.A. 102 6 2005 2052 2057
155. S. Domcke Nat. Commun. 4 2013 2126
156. J.P. Gillet, S. Varma, and M.M. Gottesman J. Natl. Cancer Inst. 105 7 2013 452 458