Current publications of the ZML

2023

Investigating the Potential of Drift Tube Ion Mobility for the Analysis of Oxidized Lipids. Silva, K. M. D., Wölk, M., Nepachalovich, P., Iturrospe, E., Covaci, A., Nuijs, A. L. N. V. & Fedorova, M., 12 Sept 2023, In: Analytical Chemistry. 95, 36, 9 p.

 Analytical Toolbox to Unlock the Diversity of Oxidized Lipids. Wölk, M., Prabutzki, P. & Fedorova, M., Apr 2023, In: Accounts of Chemical Research. 56, 7, p. 835–845 11 p.

Guiding the choice of informatics software and tools for lipidomics research applications. Ni, Z., Wölk, M., Jukes, G., Mendivelso Espinosa, K., Ahrends, R., Aimo, L., Alvarez-Jarreta, J., Andrews, S., Andrews, R., Bridge, A., Clair, G. C., Conroy, M. J., Fahy, E., Gaud, C., Goracci, L., Hartler, J., Hoffmann, N., Kopczyinki, D., Korf, A., Lopez-Clavijo, A. F., & 14 others, Feb 2023, In: Nature methods. 20, 2, p. 193-204 12 p.

 7-Dehydrocholesterol is an endogenous suppressor of ferroptosis. Fedorova, M., Nepachalovich, P., Freitas, F. P., Conrad, M., Bornkamm, G., Horling, A., Wehmann, A., Pratt, D., Garcia-Saez, A., Bargou, R., Bommert, K., Weigand, I., Kroiss, M., Meierjohann, S., Mirnics, K., Genaro-Mattos, T. C., Kumar, L., Klein-Seetharaman, J., Miyamoto, S., Imming, P., & 11 others, 2023, (Accepted/In press) In: Nature.

Membrane epilipidome – lipid modifications, their dynamics and functional significance. Fedorova, M. & Penkov, S., 2023, (Accepted/In press) The Biology of Lipids, 2nd ed.. Simons, K. & Parton, R. (eds.). Cold Spring Harbor Perspectives

2022

Synaptotagmin-13 orchestrates pancreatic endocrine cell egression and islet morphogenesis. Bakhti, M., Bastidas-Ponce, A., Tritschler, S., Czarnecki, O., Tarquis-Medina, M., Nedvedova, E., Jaki, J., Willmann, S. J., Scheibner, K., Cota, P., Salinno, C., Boldt, K., Horn, N., Ueffing, M., Burtscher, I., Theis, F. J., Coskun, Ü. & Lickert, H., Dec 2022, In: Nature communications. 13, 1, 4540.

Analytical and computational workflow for in-depth analysis of oxidized complex lipids in blood plasma. Criscuolo, A., Nepachalovich, P., Garcia-Del Rio, D. F., Lange, M., Ni, Z., Baroni, M., Cruciani, G., Goracci, L., Blüher, M. & Fedorova, M., 1 Nov 2022, In: Nature communications. 13, 1, p. 6547

Introducing the Lipidomics Minimal Reporting Checklist. McDonald, J. G., Ejsing, C. S., Kopczynski, D., Holčapek, M., Aoki, J., Arita, M., Arita, M., Baker, E. S., Bertrand-Michel, J., Bowden, J. A., Brügger, B., Ellis, S. R., Fedorova, M., Griffiths, W. J., Han, X., Hartler, J., Hoffmann, N., Koelmel, J. P., Köfeler, H. C., Mitchell, T. W., & 12 others, Sept 2022, In: Nature metabolism. 4, 9, p. 1086-1088 3 p.

Symmetric and asymmetric receptor conformation continuum induced by a new insulin. Xiong, X., Blakely, A., Kim, J. H., Menting, J. G., Schäfer, I. B., Schubert, H. L., Agrawal, R., Gutmann, T., Delaine, C., Zhang, Y. W., Artik, G. O., Merriman, A., Eckert, D., Lawrence, M. C., Coskun, Ü., Fisher, S. J., Forbes, B. E., Safavi-Hemami, H., Hill, C. P. & Chou, D. H. C., May 2022, In: Nature chemical biology. 18, 5, p. 511-519 9 p.

Research Techniques Made Simple: Lipidomic Analysis in Skin Research. Sochorová, M., Vávrová, K., Fedorova, M., Ni, Z., Slenter, D., Kutmon, M., Willighagen, E. L., Letsiou, S., Töröcsik, D., Marchetti-Deschmann, M., Zoratto, S., Kremslehner, C. & Gruber, F., Jan 2022, In: Journal of investigative dermatology. 142, 1, p. 4-11.e1

2021

Juggling with lipids, a game of Russian roulette. Aldrovandi M, Fedorova M, Conrad M. Trends Endocrinol Metab. 2021 Jul;32(7):463-473. doi: 10.1016/j.tem.2021.04.012. Epub 2021 May 11. PMID: 33985897 Review.

HIF2α is a direct regulator of neutrophil motility. Sormendi S, Deygas M, Sinha A, Bernard M, Krüger A, Kourtzelis I, Le Lay G, Sáez PJ, Gerlach M, Franke K, Meneses A, Kräter M, Palladini A, Guck J, Coskun Ü, Chavakis T, Vargas P, Wielockx B. Blood. 2021 Jun 17;137(24):3416-3427. doi: 10.1182/blood.2020007505. PMID: 33619535

Interpreting the lipidome: bioinformatic approaches to embrace the complexity. Kyle JE, Aimo L, Bridge AJ, Clair G, Fedorova M, Helms JB, Molenaar MR, Ni Z, Orešič M, Slenter D, Willighagen E, Webb-Robertson BM. Metabolomics. 2021 Jun 6;17(6):55. doi: 10.1007/s11306-021-01802-6. PMID: 34091802 Review.

The RNA binding protein human antigen R is a gatekeeper of liver homeostasis. Subramanian P, Gargani S, Palladini A, Chatzimike M, Grzybek M, Peitzsch M, Papanastasiou AD, Pyrina I, Ntafis V, Gercken B, Lesche M, Petzold A, Sinha A, Nati M, Thangapandi VR, Kourtzelis I, Andreadou M, Witt A, Dahl A, Burkhardt R, Haase R, Domingues AMJ, Henry I, Zamboni N, Mirtschink P, Chung KJ, Hampe J, Coskun Ü, Kontoyiannis DL, Chavakis T. Hepatology. 2021 Sep 14. doi: 10.1002/hep.32153. Online ahead of print. PMID: 34519101

AdipoAtlas: A reference lipidome for human white adipose tissue. Lange M, Angelidou G, Ni Z, Criscuolo A, Schiller J, Blüher M, Fedorova M. Cell Rep Med. 2021 Sep 22;2(10):100407. doi: 10.1016/j.xcrm.2021.100407. eCollection 2021 Oct 19. PMID: 34755127

Inceptor counteracts insulin signalling in β-cells to control glycaemia. Ansarullah, Jain C, Far FF, Homberg S, Wißmiller K, von Hahn FG, Raducanu A, Schirge S, Sterr M, Bilekova S, Siehler J, Wiener J, Oppenländer L, Morshedi A, Bastidas-Ponce A, Collden G, Irmler M, Beckers J, Feuchtinger A, Grzybek M, Ahlbrecht C, Feederle R, Plettenburg O, Müller TD, Meier M, Tschöp MH, Coskun Ü, Lickert H. Nature. 2021 Feb;590(7845):326-331. doi: 10.1038/s41586-021-03225-8. Epub 2021 Jan 27. PMID: 33505018

Quality control requirements for the correct annotation of lipidomics data. Köfeler HC, Eichmann TO, Ahrends R, Bowden JA, Danne-Rasche N, Dennis EA, Fedorova M, Griffiths WJ, Han X, Hartler J, Holčapek M, Jirásko R, Koelmel JP, Ejsing CS, Liebisch G, Ni Z, O'Donnell VB, Quehenberger O, Schwudke D, Shevchenko A, Wakelam MJO, Wenk MR, Wolrab D, Ekroos K. Nat Commun. 2021 Aug 6;12(1):4771. doi: 10.1038/s41467-021-24984-y. PMID: 34362906

Nonalcoholic fatty liver disease stratification by liver lipidomics. Vvedenskaya O, Rose TD, Knittelfelder O, Palladini A, Wodke JAH, Schuhmann K, Ackerman JM, Wang Y, Has C, Brosch M, Thangapandi VR, Buch S, Züllig T, Hartler J, Köfeler HC, Röcken C, Coskun Ü, Klipp E, von Schoenfels W, Gross J, Schafmayer C, Hampe J, Pauling JK, Shevchenko A. J Lipid Res. 2021;62:100104. doi: 10.1016/j.jlr.2021.100104. Epub 2021 Aug 10. PMID: 34384788

The clinical translation of eicosanoids and other oxylipins, although challenging, should be actively pursued. Gladine C, Fedorova M. J Mass Spectrom Adv Clin Lab. 2021 Aug 25;21:27-30. doi: 10.1016/j.jmsacl.2021.08.003. eCollection 2021 Aug. PMID: 34820674

Cytoplasmic condensation induced by membrane damage is associated with antibiotic lethality. Wong F, Stokes JM, Cervantes B, Penkov S, Friedrichs J, Renner LD, Collins JJ. Nat Commun. 2021 Apr 19;12(1):2321. doi: 10.1038/s41467-021-22485-6. PMID: 33875652

BioPAN: a web-based tool to explore mammalian lipidome metabolic pathways on LIPID MAPS. Gaud C, C Sousa B, Nguyen A, Fedorova M, Ni Z, O'Donnell VB, Wakelam MJO, Andrews S, Lopez-Clavijo AF. F1000Res. 2021 Jan 6;10:4. doi: 10.12688/f1000research.28022.2. eCollection 2021. PMID: 33564392

Protective Role of Sphingomyelin in Eye Lens Cell Membrane Model against Oxidative Stress. Ravandeh M, Coliva G, Kahlert H, Azinfar A, Helm CA, Fedorova M, Wende K. Biomolecules. 2021 Feb 13;11(2):276. doi: 10.3390/biom11020276. PMID: 33668553

Dynamic posttranslational modifications of cytoskeletal proteins unveil hot spots under nitroxidative stress. Griesser E, Vemula V, Mónico A, Pérez-Sala D, Fedorova M. Redox Biol. 2021 Aug;44:102014. doi: 10.1016/j.redox.2021.102014. Epub 2021 May 24. PMID: 34062408

Lipid composition dictates the rate of lipid peroxidation in artificial lipid droplets. Lange M, Wagner PV, Fedorova M. Free Radic Res. 2021 Apr;55(4):469-480. doi: 10.1080/10715762.2021.1898603. Epub 2021 Apr 19. PMID: 33866899

A Novel Technique for Redox Lipidomics Using Mass Spectrometry: Application on Vegetable Oils Used to Fry Potatoes. Koelmel JP, Aristizabal-Henao JJ, Ni Z, Fedorova M, Kato S, Otoki Y, Nakagawa K, Lin EZ, Godri Pollitt KJ, Vasiliou V, Guingab JD, Garrett TJ, Williams TL, Bowden JA, Penumetcha M. J Am Soc Mass Spectrom. 2021 Jul 7;32(7):1798-1809. doi: 10.1021/jasms.1c00150. Epub 2021 Jun 7. PMID: 34096708

older (selection)

Cryo-EM structure of the complete and ligand-saturated insulin receptor ectodomain. Gutmann T, Schäfer IB, Poojari C, Brankatschk B, Vattulainen I, Strauss M, Coskun Ü. J Cell Biol. 2020 Jan 6;219(1):e201907210. doi: 10.1083/jcb.201907210. PMID: 31727777

Computational solutions in redox lipidomics - Current strategies and future perspectives. Ni Z, Goracci L, Cruciani G, Fedorova M. Free Radic Biol Med. 2019 Nov 20;144:110-123. doi: 10.1016/j.freeradbiomed.2019.04.027. Epub 2019 Apr 26. PMID: 31035005 Review.

Live-cell lipid biochemistry reveals a role of diacylglycerol side-chain composition for cellular lipid dynamics and protein affinities. Schuhmacher M, Grasskamp AT, Barahtjan P, Wagner N, Lombardot B, Schuhmacher JS, Sala P, Lohmann A, Henry I, Shevchenko A, Coskun Ü, Walter AM, Nadler A. Proc Natl Acad Sci U S A. 2020 Apr 7;117(14):7729-7738. doi: 10.1073/pnas.1912684117. Epub 2020 Mar 25. PMID: 32213584

Comprehensive and quantitative analysis of white and brown adipose tissue by shotgun lipidomics. Grzybek M, Palladini A, Alexaki VI, Surma MA, Simons K, Chavakis T, Klose C, Coskun Ü. Mol Metab. 2019 Apr;22:12-20. doi: 10.1016/j.molmet.2019.01.009. Epub 2019 Jan 30. PMID: 30777728

DEL-1 promotes macrophage efferocytosis and clearance of inflammation. Kourtzelis I, Li X, Mitroulis I, Grosser D, Kajikawa T, Wang B, Grzybek M, von Renesse J, Czogalla A, Troullinaki M, Ferreira A, Doreth C, Ruppova K, Chen LS, Hosur K, Lim JH, Chung KJ, Grossklaus S, Tausche AK, Joosten LAB, Moutsopoulos NM, Wielockx B, Castrillo A, Korostoff JM, Coskun Ü, Hajishengallis G, Chavakis T. Nat Immunol. 2019 Jan;20(1):40-49. doi: 10.1038/s41590-018-0249-1. Epub 2018 Nov 19. PMID: 30455459

Modulation of Myelopoiesis Progenitors Is an Integral Component of Trained Immunity. Mitroulis I, Ruppova K, Wang B, Chen LS, Grzybek M, Grinenko T, Eugster A, Troullinaki M, Palladini A, Kourtzelis I, Chatzigeorgiou A, Schlitzer A, Beyer M, Joosten LAB, Isermann B, Lesche M, Petzold A, Simons K, Henry I, Dahl A, Schultze JL, Wielockx B, Zamboni N, Mirtschink P, Coskun Ü, Hajishengallis G, Netea MG, Chavakis T. Cell. 2018 Jan 11;172(1-2):147-161.e12. doi: 10.1016/j.cell.2017.11.034. PMID: 29328910

Visualization of ligand-induced transmembrane signaling in the full-length human insulin receptor. Gutmann T, Kim KH, Grzybek M, Walz T, Coskun Ü. J Cell Biol. 2018 May 7;217(5):1643-1649. doi: 10.1083/jcb.201711047. Epub 2018 Feb 16. PMID: 29453311

A Temperature-Dependent Switch in Feeding Preference Improves Drosophila Development and Survival in the Cold. Brankatschk M, Gutmann T, Knittelfelder O, Palladini A, Prince E, Grzybek M, Brankatschk B, Shevchenko A, Coskun Ü, Eaton S. Dev Cell. 2018 Sep 24;46(6):781-793.e4. doi: 10.1016/j.devcel.2018.05.028. PMID: 30253170

Preface to the Special Issue on 4-Hydroxynonenal and Related Lipid Oxidation Products.Fedorova M, Zarkovic N. Free Radic Biol Med. 2017 Oct;111:1. doi: 10.1016/j.freeradbiomed.2017.05.017. Epub 2017 May 24. PMID: 28552693

LPPtiger software for lipidome-specific prediction and identification of oxidized phospholipids from LC-MS datasets. Ni Z, Angelidou G, Hoffmann R, Fedorova M. Sci Rep. 2017 Nov 9;7(1):15138. doi: 10.1038/s41598-017-15363-z. PMID: 29123162

LipidHunter Identifies Phospholipids by High-Throughput Processing of LC-MS and Shotgun Lipidomics Datasets. Ni Z, Angelidou G, Lange M, Hoffmann R, Fedorova M. Anal Chem. 2017 Sep 5;89(17):8800-8807. doi: 10.1021/acs.analchem.7b01126. Epub 2017 Aug 8. PMID: 28753264

Cross-talk between lipid and protein carbonylation in a dynamic cardiomyocyte model of mild nitroxidative stress. Griesser E, Vemula V, Raulien N, Wagner U, Reeg S, Grune T, Fedorova M. Redox Biol. 2017 Apr;11:438-455. doi: 10.1016/j.redox.2016.12.028. Epub 2016 Dec 28. PMID: 28086193

Calcium Directly Regulates Phosphatidylinositol 4,5-Bisphosphate Headgroup Conformation and Recognition. Bilkova E, Pleskot R, Rissanen S, Sun S, Czogalla A, Cwiklik L, Róg T, Vattulainen I, Cremer PS, Jungwirth P, Coskun Ü. J Am Chem Soc. 2017 Mar 22;139(11):4019-4024. doi: 10.1021/jacs.6b11760. Epub 2017 Mar 7. PMID: 28177616