There has been a recent explosion in the study of lipid mediated signal transduction and cell regulation. The over-riding paradigm has evolved from a reductionist approach and has focused on modular signaling whereby one stimulus regulates one enzyme resulting in the generation of one active molecule. However, the complexity of lipid metabolism far exceeds a simple collection of individual signaling modules such that one agonist may regulate several enzymes or the bioactive product of one enzyme (e.g. ceramide) may serve as a substrate for another enzyme generating a different bioactive molecule (such as diacylglycerol or sphingosine). Thus, we hypothesize that the complexity of lipid metabolism serves to provide a highly regulated and coordinated network of bioactive molecules with distinct and overlapping functions. This network then serves to integrate and coordinate complex responses of cells to various agents and environmental stimuli. This proposal will test the specific hypothesis that the sphingolipid sub-universe of cell regulation in S. cerevisiae constitutes a relatively discrete domain that allows the elucidation of biochemical regulation as well as integrative approaches. We propose that a combined reductionist and integrative mathematical and systems biology approach generates novel insights into lipid-mediated cell regulation and allows the dissection of specific pathways mechanistically and functionally... Thus, we aim to 1. Develop an integromics approach in order to dissect specific sphingolipid-mediated pathways in S. cerevisiae in response to specific perturbations of sphingolipid metabolism;2. Develop an advanced model of yeast sphingolipid metabolism that focuses on distinguishing individual ceramide species;and 3. Establish specific pathways of sphingolipid-mediated cell regulation. These studies will lay the groundwork for a """"""""global"""""""" model of sphingolipid metabolism in which we may be able to predict specific metabolic and transcriptional responses that are regulated by individual sphingolipids. Subsequently, such an approach may allow us to predict the overall genetic response to a specific """"""""configuration"""""""" of sphingolipid levels. This model system could then serve as a conceptual and practical platform to extend our hypotheses to other lipid classes, followed by other aspects of regulated metabolism (metabolomic level). Such approaches will prove critical in understanding the intricate, multi-level regulation of human pathobiology where bioactive lipids play key roles in such diseases as diabetes, neurodegeneration, cancer, and inflammation.

Public Health Relevance

The metabolism of lipids is very complex yet it is critical as many lipids are functional molecules that affect the function of the cell and the body, and are involved in diseases such as diabetes, neurodegeneration, cancer, and inflammation. We have assembled a team of biochemists, molecular biologists, mathematical modelers, and system biologists in order to define novel approaches by which we can organize our knowledge on lipid metabolism and enable research that deciphers the function of individual lipids.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
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Special Emphasis Panel (ZRG1-BCMB-B (02))
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Chin, Jean
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State University New York Stony Brook
Family Medicine
Schools of Medicine
Stony Brook
United States
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Vilaça, Rita; Barros, Ivo; Matmati, Nabil et al. (2018) The ceramide activated protein phosphatase Sit4 impairs sphingolipid dynamics, mitochondrial function and lifespan in a yeast model of Niemann-Pick type C1. Biochim Biophys Acta Mol Basis Dis 1864:79-88
Chen, Po-Wei; Fonseca, Luis L; Hannun, Yusuf A et al. (2016) Analysis of the Involvement of Different Ceramide Variants in the Response to Hydroxyurea Stress in Baker's Yeast. PLoS One 11:e0146839
Chen, Po-Wei; Fonseca, Luis L; Hannun, Yusuf A et al. (2015) Dynamics of the Heat Stress Response of Ceramides with Different Fatty-Acyl Chain Lengths in Baker's Yeast. PLoS Comput Biol 11:e1004373
Montefusco, David J; Matmati, Nabil; Hannun, Yusuf A (2014) The yeast sphingolipid signaling landscape. Chem Phys Lipids 177:26-40
Qin, Tingting; Matmati, Nabil; Tsoi, Lam C et al. (2014) Finding pathway-modulating genes from a novel Ontology Fingerprint-derived gene network. Nucleic Acids Res 42:e138
Spincemaille, Pieter; Matmati, Nabil; Hannun, Yusuf A et al. (2014) Sphingolipids and mitochondrial function in budding yeast. Biochim Biophys Acta 1840:3131-7
Swinnen, Erwin; Wilms, Tobias; Idkowiak-Baldys, Jolanta et al. (2014) The protein kinase Sch9 is a key regulator of sphingolipid metabolism in Saccharomyces cerevisiae. Mol Biol Cell 25:196-211
Vilaça, Rita; Silva, Elísio; Nadais, André et al. (2014) Sphingolipid signalling mediates mitochondrial dysfunctions and reduced chronological lifespan in the yeast model of Niemann-Pick type C1. Mol Microbiol 91:438-51
Chen, Po-Wei; Fonseca, Luis L; Hannun, Yusuf A et al. (2013) Coordination of rapid sphingolipid responses to heat stress in yeast. PLoS Comput Biol 9:e1003078
Matmati, Nabil; Metelli, Alessandra; Tripathi, Kaushlendra et al. (2013) Identification of C18:1-phytoceramide as the candidate lipid mediator for hydroxyurea resistance in yeast. J Biol Chem 288:17272-84

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