Deciphering the duality of clock and growth metabolism in a cell autonomous system using NMR profiling of the secretome

Metabolites

Volumn 6, Issue 3, 2016, Pages

  Sengupta, Arjun ^a   Krishnaiah, Saikumari Y ^a   Rhoades, Seth ^a   Growe, Jacqueline ^a   Slaff, Barry ^a   Venkataraman, Anand ^a,d   Olarerin George, Anthony O ^a   Van Dang, Chi ^b   Hogenesch, John B ^a,c   Weljie, Aalim M ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

^c UNIVERSITY OF CINCINNATI   (United States)

^d JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Circadian oscillations; Detrending; Metabolomics; NMR spectroscopy; U2 OS

Indexed keywords

ARTICLE; CLUSTER ANALYSIS; DISCRIMINANT ANALYSIS; GENE EXPRESSION; HUMAN; HUMAN CELL; METABOLOMICS; NUCLEAR MAGNETIC RESONANCE IMAGING; PROTON NUCLEAR MAGNETIC RESONANCE; TEMPORAL ANALYSIS;

EID: 85006197429     PISSN: None     EISSN: 22181989     Source Type: Journal    
DOI: 10.3390/metabo6030023     Document Type: Article

References (29)

1. Buhr, E.D.; Takahashi, J.S. Molecular Components of the Mammalian Circadian Clock. In Handbook of Experimental Pharmacology 217 Circadian Clocks; Kramer, A., Merrow, M., Eds.; Springer: Berlin, Germany, 2013.
2. Antunes, L.C.; Levandovski, R.; Dantas, G.; Caumo, W.; Hidalgo, M.P. Obesity and shift work: Chronobiological aspects. Nutr. Res. Rev. 2010, 23, 155-168. [CrossRef] [PubMed]
3. Bechtold, D.A.; Gibbs, J.E.; Loudon, A.S.I. Circadian dysfunction in disease. Trends Pharmacol. Sci. 2010, 31, 191-198. [CrossRef] [PubMed]
4. Kawachi, I.; Colditz, G.A.; Stampfer, M.J.; Willett, W.C.; Manson, J.E.; Speizer, F.E.; Hennekens, C.H. Prospective Study of Shift Work and Risk of Coronary Heart Disease in Women. Circulation 1995, 92, 3178-3182. [CrossRef] [PubMed]
5. Parkes, K.R. Shift work and age as interactive predictors of body mass index among offshore workers. Scand. J. Work Environ. Health 2002, 28, 64-71. [CrossRef] [PubMed]
6. Reppert, S.M.; Weaver, D.R. Coordination of circadian timing in mammals. Nature 2002, 418, 935-941. [CrossRef] [PubMed]
7. Sharifian, A.; Farahani, S.; Pasalar, P.; Gharavi, M.; Aminian, O. Shift work as an oxidative stressor. J. Circadian Rhythms 2005, 3, 15. [CrossRef] [PubMed]
8. Bass, J.; Takahashi, J.S. Circadian integration of metabolism and energetics. Science 2010, 330, 1349-1354. [CrossRef] [PubMed]
9. Hughes, M.E.; DiTacchio, L.; Hayes, K.R.; Vollmers, C.; Pulivarthy, S.; Baggs, J.E.; Panda, S.; Hogenesch, J.B. Harmonics of Circadian Gene Transcription in Mammals. PLoS Genet. 2009, 5, e1000442. [CrossRef] [PubMed]
10. Krishnaiah, S.Y.; Wu, G.; Growe, J.; Rhodes, S.; Coldren, F.; Venkataraman, A.; George, A.O.O.; Francey, L.J.; Er, U.; Sianati, B. et al. Clock regulation of liver- and cell-autonomous metabolism reveals decoupling between transcription and metabolism. Cell Metabolism 2016. Under Review.
11. Altman, B.J.; Hsieh, A.L.; Sengupta, A.; Krishnanaiah, S.Y.; Stine, Z.E.; Walton, Z.E.; Gouw, A.M.; Venkataraman, A.; Li, B.; Goraksha-Hicks, P. et al. MYC Disrupts the Circadian Clock and Metabolism in Cancer Cells. Cell Metab. 2015, 22, 1009-1019. [CrossRef] [PubMed]
12. Smolinska, A.; Blanchet, L.; Buydens, L.M.C.; Wijmenga, S.S. NMR and pattern recognition methods in metabolomics: From data acquisition to biomarker discovery: A review. Anal. Chim. Acta 2012, 750, 82-97. [CrossRef] [PubMed]
13. Weljie, A.M.; Newton, J.; Mercier, P.; Carlson, E.; Slupsky, C.M. Targeted Profiling: Quantitative Analysis of 1H-NMR Metabolomics Data. Anal. Chem. 2006, 78, 4430-4442. [CrossRef] [PubMed]
14. Cermakian, N.; Boivin, D.B. A molecular perspective of human circadian rhythm disorders. Brain Res. Brain Res. Rev. 2003, 42, 204-220. [CrossRef]
15. Partch, C.L.; Green, C.B.; Takahashi, J.S. Molecular architecture of the mammalian circadian clock. Trends Cell Biol. 2014, 24, 90-99. [CrossRef] [PubMed]
16. Peirson, S.N.; Foster, R.G. Sleep and Circadian Rhythm Disruption in Psychosis. In Circadian Medicine; John Wiley & Sons Inc.: Hoboken, NJ, USA, 2015; pp. 271-282.
17. Lauretti, E.; Di Meco, A.; Merali, S.; Praticò, D. Circadian rhythm dysfunction: A novel environmental risk factor for Parkinson’s disease. Mol. Psychiatry 2016. [CrossRef] [PubMed]
18. Erion, R.; King, A.N.; Wu, G.; Hogenesch, J.B.; Sehgal, A. Neural clocks and Neuropeptide F/Y regulate circadian gene expression in a peripheral metabolic tissue. Elife 2016, 5, e13552. [CrossRef] [PubMed]
19. Jang, C.; Lahens, N.F.; Hogenesch, J.B.; Sehgal, A. Ribosome profiling reveals an important role for translational control in circadian gene expression. Genome Res. 2015, 25, 1836-1847. [CrossRef] [PubMed]
20. Mehta, M.; Sonawat, H.M.; Sharma, S. Malaria parasite-infected erythrocytes inhibit glucose utilization in uninfected red cells. FEBS Lett. 2005, 579, 6151-6158. [CrossRef] [PubMed]
21. Dabos, K.J.; Parkinson, J.A.; Hewage, C.; Nelson, L.J.; Sadler, I.H.; Hayes, P.C.; Plevris, J.N. 1H-NMR spectroscopy as a tool to evaluate key metabolic functions of primary porcine hepatocytes after cryopreservation. NMR Biomed. 2002, 15, 241-250. [CrossRef] [PubMed]
22. Drago, D.; Cossetti, C.; Iraci, N.; Gaude, E.; Musco, G.; Bachi, A.; Pluchino, S. The stem cell secretome and its role in brain repair. Biochimie 2013, 95, 2271-2285. [CrossRef] [PubMed]
23. Uyar, A.; Seli, E. Metabolomic assessment of embryo viability. Semin. Reprod. Med. 2014, 32, 141-152. [CrossRef] [PubMed]
24. Booth, S.C.; Weljie, A.M.; Turner, R.J. Metabolomics reveals differences of metal toxicity in cultures of Pseudomonas pseudoalcaligenes KF707 grown on different carbon sources. Front. Microbiol. 2015, 6, 827. [CrossRef] [PubMed]
25. Nagoshi, E.; Saini, C.; Bauer, C.; Laroche, T.; Naef, F.; Schibler, U. Circadian Gene Expression in Individual Fibroblasts: Cell-Autonomous and Self-Sustained Oscillators Pass Time to Daughter Cells. Cell 2004, 119, 693-705. [CrossRef] [PubMed]
26. Leise, T.L. Wavelet analysis of circadian and ultradian behavioral rhythms. J. Circadian Rhythms 2013, 11, 5. [CrossRef] [PubMed]
27. Baggs, J.E.; Price, T.S.; DiTacchio, L.; Panda, S.; Fitzgerald, G.A.; Hogenesch, J.B. Network features of the mammalian circadian clock. PLoS Biol. 2009, 7, e52. [CrossRef] [PubMed]
28. 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]
29. Tambellini, N.P.; Zaremberg, V.; Turner, R.J.; Weljie, A.M. Evaluation of extraction protocols for simultaneous polar and non-polar yeast metabolite analysis using multivariate projection methods. Metabolites 2013, 3, 592-605. [CrossRef] [PubMed]