Integration of lipidomics and transcriptomics data towards a systems biology model of sphingolipid metabolism

BMC Systems Biology

Volumn 5, Issue , 2011, Pages

  Gupta, Shakti ^a   Maurya, Mano R ^a   Merrill Jr, Alfred H ^b   Glass, Christopher K ^a   Subramaniam, Shankar ^a,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MAMMALIA;

SPHINGOLIPID;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; BIOSYNTHESIS; CELL LINE; METABOLISM; METHODOLOGY; MOUSE; SYSTEMS BIOLOGY;

ANIMALS; CELL LINE; METABOLIC NETWORKS AND PATHWAYS; MICE; MODELS, BIOLOGICAL; SPHINGOLIPIDS; SYSTEMS BIOLOGY;

EID: 79551688548     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-5-26     Document Type: Article

References (35)

1. Fahy E, Subramaniam S, Brown HA, Glass CK, Merrill AH, Murphy RC, Raetz CRH, Russell DW, Seyama Y, Shaw W, et al. A comprehensive classification system for lipids. Journal of lipid research 2005, 46(5):839-862. 10.1194/jlr.E400004-JLR200, 15722563.
2. Merrill AH, Wang MD, Park M, Sullards MC. (Glyco)sphingolipidology: an amazing challenge and opportunity for systems biology. Trends Biochem Sci 2007, 32(10):457-468. 10.1016/j.tibs.2007.09.004, 17928229.
3. Zheng W, Kollmeyer J, Symolon H, Momin A, Munter E, Wang E, Kelly S, Allegood JC, Liu Y, Peng Q, et al. Ceramides and other bioactive sphingolipid backbones in health and disease: lipidomic analysis, metabolism and roles in membrane structure, dynamics, signaling and autophagy. Biochim Biophys Acta 2006, 1758(12):1864-1884. 10.1016/j.bbamem.2006.08.009, 17052686.
4. Lopez PH, Schnaar RL. Gangliosides in cell recognition and membrane protein regulation. Curr Opin Struct Biol 2009, 19(5):549-557. 10.1016/j.sbi.2009.06.001, 2763983, 19608407.
5. Zeidan YH, Hannun YA. Translational aspects of sphingolipid metabolism. Trends Mol Med 2007, 13(8):327-336. 10.1016/j.molmed.2007.06.002, 17588815.
6. Wennekes T, van den Berg RJ, Boot RG, van der Marel GA, Overkleeft HS, Aerts JM. Glycosphingolipids--nature, function, and pharmacological modulation. Angew Chem Int Ed Engl 2009, 48(47):8848-8869. 10.1002/anie.200902620, 19862781.
7. Murphy RC, Fiedler J, Hevko J. Analysis of nonvolatile lipids by mass spectrometry. Chem Rev 2001, 101(2):479-526. 10.1021/cr9900883, 11712255.
8. KEGG BRITE database. , http://www.genome.jp/kegg/brite.html
9. SphinGOMAP pathways. , http://sphingolab.biology.gatech.edu
10. Gehlenborg N, O'Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, Kitano H, Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D, et al. Visualization of omics data for systems biology. Nat Methods 2010, 7(3 Suppl):S56-68. 10.1038/nmeth.1436, 20195258.
11. Bartke N, Hannun YA. Bioactive sphingolipids: metabolism and function. Journal of lipid research 2009, 50(Suppl):S91-96. 10.1194/jlr.R800080-JLR200, 2674734, 19017611.
12. Kitatani K, Idkowiak-Baldys J, Hannun YA. The sphingolipid salvage pathway in ceramide metabolism and signaling. Cell Signal 2008, 20(6):1010-1018. 10.1016/j.cellsig.2007.12.006, 2422835, 18191382.
13. Fyrst H, Saba JD. Sphingosine-1-phosphate lyase in development and disease: sphingolipid metabolism takes flight. Biochim Biophys Acta 2008, 1781(9):448-458. 2749932, 18558101.
14. Maceyka M, Milstien S, Spiegel S. Sphingosine-1-phosphate: the Swiss army knife of sphingolipid signaling. Journal of lipid research 2009, 50(Suppl):S272-276. 10.1194/jlr.R800065-JLR200, 2674705, 18987387.
15. Henning PA, Merrill AH, Wang MD. Dynamic pathway modeling of sphingolipid metabolism. Conf Proc IEEE Eng Med Biol Soc 2004, 4:2913-2916.
16. Alvarez-Vasquez F, Sims KJ, Cowart LA, Okamoto Y, Voit EO, Hannun YA. Simulation and validation of modelled sphingolipid metabolism in Saccharomyces cerevisiae. Nature 2005, 433(7024):425-430. 10.1038/nature03232, 15674294.
17. Henning P, Moffitt R, Allegood J, Wang E, Merrill A, Wang M. Computationally predicting rate constants in pathway models. Conf Proc IEEE Eng Med Biol Soc 2005, 5:5093-5096.
18. Garcia J, Shea J, Alvarez-Vasquez F, Qureshi A, Luberto C, Voit EO, Del Poeta M. Mathematical modeling of pathogenicity of Cryptococcus neoformans. Mol Syst Biol 2008, 4:183. 10.1038/msb.2008.17, 2387229, 18414484.
19. Kyoto Encyclopedia of Genes and Genomes (KEGG). , http://www.genome.ad.jp/kegg/
20. Junker BH, Klukas C, Schreiber F. VANTED: A system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics 2006, 7.
21. Gupta S, Maurya MR, Stephens DL, Dennis EA, Subramaniam S. An Integrated Model of Eicosanoid Metabolism and Signaling Based on Lipidomics Flux Analysis. Biophysical Journal 2009, 96(11):4542-4551. 10.1016/j.bpj.2009.03.011, 2711499, 19486676.
22. Merrill AH. Characterization of serine palmitoyltransferase activity in Chinese hamster ovary cells. Biochim Biophys Acta 1983, 754(3):284-291.
23. Sullards MC, Allegood JC, Kelly S, Wang E, Haynes CA, Park H, Chen Y, Merrill AH. Structure-specific, quantitative methods for analysis of sphingolipids by liquid chromatography-tandem mass spectrometry: "inside-out" sphingolipidomics. Methods Enzymol 2007, 432:83-115. full_text, 17954214.
24. Maurya MR, Subramaniam S. A kinetic model for calcium dynamics in RAW 264.7 cells: 1. Mechanisms, parameters, and subpopulational variability. Biophys J 2007, 93(3):709-728. 10.1529/biophysj.106.097469, 1913151, 17483174.
25. Yoshikawa K, Kita Y, Kishimoto K, Shimizu T. Profiling of eicosanoid production in the rat hippocampus during kainic acid-induced seizure: dual phase regulation and differential involvement of COX-1 and COX-2. The Journal of biological chemistry 2006, 281(21):14663-14669. 10.1074/jbc.M511089200, 16569634.
26. The Mathworks, Inc.© 1994 - 2010. , http://www.mathworks.com/
27. Dennis EA, Deems RA, Harkewicz R, Quehenberger O, Brown HA, Milne SB, Myers DS, Glass CK, Hardiman GT, Reichart D, et al. A Mouse Macrophage Lipidome. J Biol Chem 2010, 285(51):39976-39985. 10.1074/jbc.M110.182915, 20923771.
28. Messmer TO, Wang E, Stevens VL, Merrill AH. Sphingolipid biosynthesis by rat liver cells: effects of serine, fatty acids and lipoproteins. J Nutr 1989, 119(4):534-538.
29. Merrill AH, Wang E, Mullins RE. Kinetics of long-chain (sphingoid) base biosynthesis in intact LM cells: effects of varying the extracellular concentrations of serine and fatty acid precursors of this pathway. Biochemistry 1988, 27(1):340-345. 10.1021/bi00401a051, 3126810.
30. Gomez-Munoz A. Ceramide 1-phosphate/ceramide, a switch between life and death. Biochim Biophys Acta 2006, 1758(12):2049-2056. 10.1016/j.bbamem.2006.05.011, 16808893.
31. Niwa S, Graf C, Bornancin F. Ceramide kinase deficiency impairs microendothelial cell angiogenesis in vitro. Microvasc Res 2009, 77(3):389-393. 10.1016/j.mvr.2009.01.006, 19323974.
32. Hinkovska-Galcheva V, VanWay SM, Shanley TP, Kunkel RG. The role of sphingosine-1-phosphate and ceramide-1-phosphate in calcium homeostasis. Curr Opin Investig Drugs 2008, 9(11):1192-1205.
33. Pettus BJ, Kitatani K, Chalfant CE, Taha TA, Kawamori T, Bielawski J, Obeid LM, Hannun YA. The coordination of prostaglandin E2 production by sphingosine-1-phosphate and ceramide-1-phosphate. Mol Pharmacol 2005, 68(2):330-335.
34. Saxena S, Banerjee M, Shirumalla RK, Ray A. Ceramide kinase: a potential anti-inflammatory target?. Curr Opin Investig Drugs 2008, 9(5):455-462.
35. Lamour NF, Chalfant CE. Ceramide kinase and the ceramide-1-phosphate/cPLA2alpha interaction as a therapeutic target. Curr Drug Targets 2008, 9(8):674-682. 10.2174/138945008785132349, 18691014.