Bioorganic and medicinal chemistry: Understanding the involvement of lipids in different cell fates; LC-MS based lipidomics; biochemical characterization of lipids of interest
Associate Professor, 2019-2022
Jere Solo Assistant Professor, 2013-2019
Postdoctoral Research Associate, 2009-2013
Dana Farber Cancer Institute (Cancer Biology) / Harvard Medical School (Biological Chemistry and Molecular Pharmacology)
Ph.D., Biological Chemistry, 2003-2008
University of Pennsylvania, Department of Chemistry, Philadelphia, USA
B.S., Chemistry, 1998-2003
Koc University, Department of Chemistry, Istanbul, Turkey
The central theme of our research is to investigate the role of lipids in membrane-related transformations that take place during cellular processes that are important for human health and disease.
Our research program aims to functionally characterize the involvement of lipids in various decision-making processes of the cell, including cessation of cell division (replicative senescence) and death (i.e. apoptosis and necroptosis). At a fundamental level, our work investigates how subtle differences in chemical structure of lipids affect their biological function. Overall, our work aims to:
i) determine unknown functions of lipid in membrane-related phenotypes that accompany different cellular fates,
ii) identify biochemical mechanisms that results in their regulation cell fates, and
iii) targetable lipid biosynthesis-related enzyme to perturb these processes and membrane-related change that are associated with these processes.
We have a unique expertise at the interaction of bioanalytical chemistry and chemical biology. We leverage liquid chromatography-mass spectrometry-based lipidomics as a powerful discovery tool to obtain the chemical resolution we need while analyzing the changes in cellular lipidomes. We then use chemical biology and biochemistry to investigate the role of individual lipids that we prioritize based on the lipidomics.
(Please see Prof. Atilla’s google scholar page for a comprehensive list of publications:
1. Pradhan A., Lu D., Parisi L.R., Shen S., Berhane I.A., Galster S.G., Bynum K., Monje-Galvan V., Gokcumen O., Chemler S.R., Qu J., Kay J., Atilla-Gokcumen G.E.* Protein acylation by saturated very long chain fatty acids and endocytosis are involved in necroptosis. Cell Chem. Biol. 2021 DOI:10.1016/j.chembiol.2021.03.012
2. Morstein J., Kol M., Novak A.J.E., Feng S., Khayyo S., Hinnah K., Li-Purcell N., Pan G., Williams B.M., Riezman H., Atilla-Gokcumen G.E., Holthuis J., Trauner D.* Short Photoswitchable Ceramides enable Optical Control of Apoptosis. ACS Chem. Biol. 2021 DOI: 10/1021/acschembio.0c00823
3. Millner A., Lizardo D.Y., Atilla-Gokcumen G.E.*, Untargeted lipidomics highlight the depletion of deoxyceramides during therapy-induced senescence. Proteomics, 2020, 20(10):e2000013
4. Bayraktar E.C., La K., Karpman K., Unlu G., Ozdemir C., Ritter D.J., Alwaseem H., Molina H., Hoffmann H., Millner A., Atilla-Gokcumen G.E., Gamazon E.R., Rushing A.R., Knapik E.W., Basu S., Birsoy K.* Metabolic coessentiality mapping identifies C12orf49 as a regulator of SREBP processing and cholesterol metabolism. Nature Metabolism, 2020, 2(6):487-498.
5. Parisi L.R., Sowlati-Hashjin S., Berhane I.A., Carter K.A., Lovell J.F., Chemler S.R., Karttunen M., Atilla-Gokcumen G.E.* Membrane disruption by very long chain fatty acids during necroptosis. ACS Chem. Bio. 2019 14:2286-2294.
Featured in Nature Chemical Biology (2019, 15:1029)
6. Li N., Saitou M., Atilla-Gokcumen G.E.* p38 MAPK pathway is Involved in Triacylglycerol and Lipid Droplet Accumulation during Apoptosis. Proteomics, 2019, 1900160-1900167.
7. Chavez N., Montes A., Bisson M., Atilla-Gokcumen G.E.*; Aga D.S. High-resolution mass spectrometry-based metabolomics reveal the disruption of jasmonic pathway upon copper nanoparticles exposure in Arabidopsis thaliana. Sci. Total Environ. 2019 693:133443.
8. Brovkovych V., Aldrich A., Li N., Atilla-Gokcumen G.E.*, Frasor J.* Extraction of Lipids and Lipid-derived Metabolites in Probing Breast Cancer Cell Biology. Proteomics 2019, 19:1800370-1800378.
9. Chavez N.S., Aga D.S.*, Atilla-Gokcumen G.E.* Lipidomics Reveals Insights on the Biological Effects of Copper Oxide Nanoparticles on a Human Colon Carcinoma Cell Line. Mol. Omics 2019 15:30-38. Selected as cover article
10. Matich E.**, Chavez N.S.**, Aga D.S.*, Atilla-Gokcumen G. E.* Applications of Metabolomics in Assessing Ecological Effects of Emerging Contaminants and Pollutants on Plants. J. Haz. Mat. 2019, 373, 527-535.
11. Brovkovych V., Izhar Y., Danes J., Dubrovskyi O., Sakallioglu I.T., Morrow L.M., Atilla-Gokcumen G.E.*, Frasor J.* Fatostatin Induces Pro- and Anti-apoptotic Lipid Accumulation in Breast Cancer. Oncogenesis 2018 7:66.
12. Saitou M.**, Lizardo D.Y.**, Taskent R.O., Millner A., Gokcumen O.*, Atilla-Gokcumen G.E.*, An Evolutionary Transcriptomics Approach Links CD36 to Membrane Remodeling in Replicative Senescence Mol. Omics 2018 4:237-245 (formerly Mol. Biosystems). Cover article
13. Matich E., Ghafari H., Camgoz E.†, Caliskan E.†, Pfeifer B., Haznedaroglu B.Z.*, Atilla-Gokcumen G.E.*, Time Series Lipidomics Analysis of Green Microalgae under Nutrient Stress. Biotech. Biofuel., 2018, 11, 29-36.
14. Li N., Sancak Y., Frasor J.M., Atilla-Gokcumen G.E.*, A Protective Role for Triacylglycerols During Apoptosis. Biochemistry, 2018, 57, 72-80.
15. Parisi L.R., Li N., Atilla-Gokcumen G.E.*, Very Long Chain Fatty Acids are Functionally Involved in Necroptosis. Cell Chem Biol, 2017, 24, 1445-1454.
16. Chavez N., Montes A., Bisson M., Atilla-Gokcumen, G.E.*; Aga, D.S.*, Mass Spectrometry-based Metabolic Profiling to Assess Uptake and Effects of Silver Nanoparticles on Arabidopsis thaliana Env. Sci. Nano 2017, 4, 1944-1953. Cover article
17. Lizardo, D., Lin, Y.L., Gokcumen, O.*, Atilla-Gokcumen, G.E.*, Lipids are Central to Replicative Senescence. Molecular bioSystems 2107, 13 (3), 498-509. Selected as “HOT” article.
18. Matich, E., Butry, D., Ghafari, M., del Solar, V., Camgoz, E.†, Pfeifer, B.A., Aga, D.S., Haznedaroglu, B.Z., Atilla-Gokcumen, G.E.*, Mass Spectrometry-based Metabolomics of Value-added Biochemicals from Ettlia oleoabundans. Algal Res. 2016, 19, 146-54.
19. Li, N., Lizardo, D.Y., Atilla-Gokcumen, G.E.*, Specific Triacylglycerols Accumulate via Increased Lipogenesis During 5-FU-Induced Apoptosis. ACS Chem. Biol. 2016, 11 (9), 2583-7.
20. Del Solar, V., Lizardo, D.Y., Li, N., Hurst, J.J., Brais†, C.J.; Atilla-Gokcumen, G.E.*, Differential Regulation of Specific Sphingolipids in Colon Cancer Cells during Staurosporine-Induced Apoptosis. Chem. Biol. 2015, 22 (12), 1662-70.