Executive Summary
TOWARDS A EUROPEAN LIPIDOMICS PROGRAM
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TOWARDS A EUROPEAN LIPIDOMICS PROGRAMPlan for Using and Disseminating Knowledge (extended version) Final Report 2005-2007 Period covered: from 1/1/05 to 1/7/07 Date of preparation: 1/1/08 Start date of project: 1/1/05 Duration: 2.5 years Project coordinator name: Prof. Gerrit van Meer Project coordinator organisation name: Utrecht University
The objectives of the Specific Support Action were: Objective 1: To network the field of Metabolomics and to seek alliances with relevant stakeholders Objective 2: To link the field of Metabolomics to the genomics and proteomics initiatives. Objective 3: To define a strategy for Metabolomics research, using Lipidomics as an example. Objective 4: To initiate an Expertise Platform on Lipidomics Objective 5: To hold both science-related as well as policy meetings One product of the SSA is the participation of roughly one thousand scientists, clinicians and industrial stakeholders in the ELIfe workshops and meetings, and the resulting networking between them. A second product is the interactive Lipidomics Expertise Platform on the ELIfe website. A third product is formed by the papers published in the international literature. As such there are no exploitable results. Section 2 – Dissemination of knowledge
Conferences. The conferences organized under the present SSA were: 1.5 ELIfe/Special FEBS meeting - The general ELIfe meeting entitled 'New concepts in lipidology: from lipidomics to disease' (Noordwijkerhout, NL, 21-25 October 2006) was cosponsored as a FEBS special meeting (AP6a) and was attended by over 250 participants, (http://www.febslipid2006.chem.uu.nl/). The speaker selection was performed by the FEBS and ELIFE organizing committee (Ben de Kruijff, Pete Downes, Bernd Helms, Kai Simons, Gerrit van Meer (chair) and Felix Wieland), and the other ELIfe members by a written procedure. The meeting hosted a short joint symposium between the Nordrhein-Westfälische Akademie der Wissenschaften and the Dutch Royal Academy of Arts and Sciences contributed by Konrad Sandhoff, Bonn. - The meeting hosted the industry meeting (see under T3.3). - Bernd Helms and Gerrit van Meer edited a special ELIfe issue of FEBS Letters under the title "Lipidome and Disease" which was distributed at the meeting. 2.2 Mass spec workshop (Dresden, 20-21 May 2005) - This was a successful workshop on mostly technical aspects of mass spectrometry with a final discussion focusing on what is required to apply this technology to the broader field of lipidomics, especially the cell biological and medical applications. The meeting was attended by mostly mass spectroscopists. The American LIPID MAPS consortium was well-represented, and also the Japanese LipidBank consortium was represented. - In a meeting of the Executive Committee (van Meer, Schmitz, Spener, Simons) with the International Lipids Classification and Nomenclature Committee (Ed Dennis, Chris Raetz, Bob Murphy, Fritz Spener, Gerrit van Meer, Yousuke Seyama and Takao Shimizu), actually attended by Ed Dennis, Masahiro Nishijima, Gerd Schmitz, Fritz Spener, Kai Simons, Ryo Taguchi, and Gerrit van Meer, all agreed to use one common database number for any lipid. The number would be preceeded by the name of the database in which the lipid was entered. LIPID MAPS will propose a procedure for how to handle this in practice. - The workshop was also visited by the EC project officer, Christina Kyriakopoulou, who confirmed the importance of bringing the lipidomics initiative to fruition.
The EMBO/ELIfe workshop "Dynamic Lipid Organization in Cells" was held in Bilbao, 3-7 June 2006 by Kai Simons, Gisou van der Goot, Felix Goñi and Gerrit van Meer. Co-sponsoring by EMBO was requested and awarded. The workshop was advertised all over Europe. The response was great and the workshop was a big success. The workshop was attended by 120 participants and had 35 speakers from all over the world, but mostly from Europe. There were plenary discussions, poster sessions and round tables. The poster sessions worked extremely well with lots of discussions at each poster over the whole meeting. Conclusions from the workshop were that lipidomics is now ripe for funding from the next EC framework programme. The technology in mass spectrometry and also many different biophysical techniques, such as fluorescence correlation spectroscopy and single molecule microscopy are paving the way for a exploration of the functions of lipids in normal cell physiology and in disease. Europe has a very strong research base in this area, which needs to be defended. The outcome of the workshop was used as a preparation for the definition of possible spearpoints in the next EC framework programme. Questions that could be addressed are protein lipid interactions in structure biology, a role of single lipids cholesterol rafts in cellular function and disease, the role of lipid droplets in normal physiology and obesity (the latter topic has been worked out in the LipidomicNet proposal which has been selected for funding under FP7).
As decided unanimously in the Kick-off meeting, the ELIfe workshop was held as a satellite to the ICBL 2006 meeting in Pécs, 5-10 September 2006 (http://www.icbl2006.hu/). The ELIfe workshop was organized by Balázs Sarkadi and Andras Varadi (local organizers), Gerd Utermann, and Pam Fredman. It was organized in excellent collaboration with the ICBL organizer Laszlo Vigh, and with the ICBL chair (and ELIfe member) Michel Lagarde who also managed to involve the International Society for the Study of Fatty Acids and Lipids (ISSFAL). 3.3 Industry meeting Within the ELIfe/FEBS Special Meeting “New Concepts in Lipidology: from Lipidomics to Disease” two half-day sessions were devoted to “Industrial and Technological Aspects of Lipidomics”, chaired by Dr. Ron Potman (Unilever, chair of ELIfe advisory board, president of Euro Fed Lipid) and Dr. Fritz Spener (ELIfe board member, University of Graz). Speakers were either from industry or applied-research oriented academic institutions. A third short session “Lipidomics and Metabolomics” was chaired by Drs. Peter Downes and Fran Platt. Almost all speakers were present at the Round Table Discussion chaired by Dr. Spener at the end of the second half-day industrial session with more than 60 participants. The public conferences to which ELIfe contributed were: 1.3 Symposia - The speakers were asked to connect from their different background metabolomics/lipidomics with genomics/proteomics, and where possible relate their talks to medically relevant issues and industrial applications. The idea was to enthuse broad audiences of scientists from the life sciences (ELSO), industry (ISF) and biomedicine/biochemistry (ICBL) for the new developments in metabolomics/lipidomics. The ELIfe members had discussions on the continuation of the lipidomics initiative in Frankfurt, August 2006 and February 2007. 1.3.1a The ELSO 2005 conference The ELSO 2005 conference, 3-7 September in Dresden (D), was attended by 1,200 scientists, amongst whom 40% PhD students. The program consisted of 6 plenary sessions, 21 minisymposia (in 3 sessions of 7 parallel symposia), 3 poster sessions and 7 sub-group meetings. ELIfe contributed Minisymposium 1: "Lipidomics", chaired by Pam Fredman and Gerrit van Meer. After an introduction of the EC-funded European Lipidomics Initiative and scientific ELIfe presentations by the chairs, the invited lecturer Kim Ekroos (Astra-Zeneca, Mölndal, Sweden) presented a lecture entitled "Unravelling phospholipidomes and sphingolipidomes by lipid profiling". This was followed by three presentations selected from the poster abstracts. The minisymposium was attended by over 100 participants. The purpose of having this session was to expose a broad audience of life scientists including many young scientists to lipidomics from three different angles, basic (van Meer), medical (Fredman) and industry (Ekroos) and to try and make them enthusiastic for this upcoming field. This field can only develop in its whole breadth if young scientists from different disciplines join in. The lecturers were available for discussion at this networking meeting for one more day.
- Unexpectedly, ELSO did not organize its meeting in 2006. Instead, ELIfe contributed a session to the 4th Euro Fed Lipid Congress – Fats, Oils and Lipids for a Healthier Future, Madrid, Spain (October 1-4, 2006). One 4 hour session was contributed on Lipid Mediators and Lipidomics, chaired by Fritz Spener and Michel Lagarde (http://www.eurofedlipid.org/meetings/madrid/). This was a meeting with an industrial character. 1.3.2a International Society for Fat Research At the 26th World Congress and Exhibition of the International Society for Fat Research in Prague, Czech Republic, 25-28 September 2005, hosted by the Czech Chemical Society and Euro Fed Lipid: 26th ISF World Congress "Modern aspects of fats and oils--A fascinating source of knowledge", the session on "Lipid Bioscience and Genomics" was sponsored by ELIfe. It was chaired by Fritz Spener and J. Kas: - Ben van Ommen, Project coordinator of NUGO (www.nugo.org/metabolomics), TNO Nutrition and Food Research, Zeist, NL: "Food and health approached by lipidomics and nutrigenomics". - David A. Bernlohr, University of Minnesota, Minneapolis, MN, USA: "Proteomics of lipid oxidation in diabetes and obesity". The International Society for Fat Research and the European Federation for the Science and Technology of Lipids, like the American Oil Chemists Society have a strong industrial character, meaning that their activities are industry oriented and are rarely attended by life scientists and clinical scientists.
- ELIfe contributed to the 47th International Conference on the Bioscience of Lipids (ICBL - ELIfe - ILPS) joint meeting, 5-10 September, 2006 in Pécs, Hungary (http://www.icbl2006.hu). One full day was dedicated to two joint ICBL-ELIfe sessions on Lipidomics and Membrane microdomains, co-chaired by Gerd Schmitz, Gabor Balogh, Gerrit van Meer and Janos Szöllõsi. In the joint ICBL–ELIfe session on Lipidomics, Markus Wenk of National University of Singapore discussed lipidomics of host-pathogen interactions. Edward A. Dennis, University of California at San Diego, La Jolla CA, USA, told about the progress in LIPID MAPS and eicosanoid lipidomics. Gerd Schmitz of University of Regensburg, Germany, focussed on the effect of differential raft regulation in human macrophages upon Ox-LDL and E-LDL loading. In the session Membrane Microdomains, Janos Szollosi of the Hungarian Academy of Sciences, Debrecen, Hungary, told that membrane microdomains are distinct molecular association clusters with function properties. Gerhard Schütz of Johannes Keppler University Linz, Austria, had a look onto the nanoscopic organization of the plasma membrane using single molecule microscopy. Unfortunately, Akihiro Kusumi of Nagoya University could not attend the meeting. His plenary talk was replaced by Toshihide Kobayashi, Riken, Japan. He introduced the combination of different novel cholesterol probes with the capability to reveal the cholesterol gradient in cell membranes. Finally, Gerrit van Meer of Utrecht University, The Netherlands, discussed dynamic organization and unexpected function of typical raft lipids. Papers 2005:
1.a Fahy, E., S. Subramaniam, H.A. Brown, C.K. Glass, A.H. Merrill, Jr., R.C. Murphy, C.R. Raetz, D.W. Russell, Y. Seyama, W. Shaw, T. Shimizu, F. Spener, G. van Meer, M.S. Vannieuwenhze, S.H. White, J. Witztum, and E.A. Dennis (2005) A comprehensive classification system for lipids. J. Lipid Res. 46, 839-861. 1.b idem: (2005) Eur. J. Lipid Sci. Technol. 107, 337-364 2. Varfolomeyev, S., Efremenko, E., Beletskaya, I., Bertini, I., Blackburn, G.M., Bogdanov, A., Cunin, R., Eichler, J., Galaev, I., Gladyshev, V., O’Hagan, D., Haertle, T., Jarv, J., Karyakin, A., Kurochkin, I., Mikolajczyk, M., Poroikov, V., Sakharov, I., Spener, F., Voyer, N., and Wild, J. (2005) Postgenomic chemistry (IUPAC Technical Report). Pure Appl. Chem. 77, 1641–1654. 3. Spener F. (2005) European Commission funds lipidomics project. Eur. J. Lipid Sci. Technol. 107, 1-2. 4. Spener F. (2005) Lipidomics and consequences: a new classification system for lipids. Eur. J. Lipid Sci. Technol. 107, 277-278. 5. van Meer, G. (2005) Cellular Lipidomics. EMBO J. 24, 3159-3165. 2006: 1. Griffiths, W. (2006) Why steroidomics in brain? Eur. J. Lipid Sci. Technol. 108, 707–708. 2. Helms, B. (2006) Host-Pathogen interactions: Lipids grease the way. Eur. J. Lipid Sci. Technol. 108, 895–897. 3. Schmitz, G., Liebisch, G., Langmann, T. (2006) Lipidomic strategies to study structural and functional defects of ABC-transporters in cellular lipid trafficking. FEBS Lett. 580, 5597-5610. 4. Spener, F., Kohlwein, S.D., and Schmitz, G. (2006) Lipid droplets and lamellar bodies – from innocent bystanders to prime targets of lipid research for combating human diseases. Eur. J. Lipid Sci. Technol. 108, 541-543. 5. Spener, F., Zechner, R., and Borlak, J. (2006) Is lipotoxicity an oxymoron? Eur. J. Lipid Sci. Technol. 108, 625-627. 6. van Meer, G. (2006) How do sphingolipids and lipid rafts relate to pathology? Eur. J. Lipid Sci. Technol. 108, 799–801. 7. van Meer, G., Leeflang, B.R., Liebisch, G,. Schmitz, G., Goni, F.M. (2007) The European lipidomics initiative: enabling technologies. Methods Enzymol. 432, 213-232. 8. Helms, B. and van Meer, G., eds. (2006) Lipidome and Disease. FEBS Letters Special Issue. FEBS Lett. 580, 5429-5610. A special ELIfe issue of FEBS Letters "Lipidome and Disease", edited by Gerrit van Meer and Bernd Helms, drawing attention to the general meeting and the ELIfe activities, distributed at the ELife/FEBS meeting. 9. van Meer, G. and Spener, F. (Co-Chairs), Leeflang, B.R. (Secretary), Beisiegel, U., Bougnoux, P., Goñi, F., Griffiths, W., Hartmann, T., Helms, B., Hoekstra, D., Julià-Sapé, M., Larijani, B., Moschetta, A., Mouritsen, O.G., Norata, G.D., Payrastre, B., Record, M., Schmitz, G., Simons, K., Tselepis, A., Vaz, W., Vigh, L., Voelker, D.R., Wakelam, M.J.O., and Wanders, R.J.A. (2008) Structural Medicine II: the Importance of Lipidomics for Health and Disease, European Science Foundation Policy Briefing, in press. The policy briefing specifically acknowledges EC specific support action LSSG-CT-2004-013032. 10. van Meer, G. (main proposer), Malhotra, V., Marsh, M., Simons, K., van der Goot, G., Warren, G. (2008) Membrane Architecture and Dynamics (EuroMembrane), EuroCore theme proposal. Call to be launched in spring 2008. Interviews: L. Winckler (2005) Lipidomics. Laborjournal 12, 20-23. A paper aimed at the general biomedical community and based on interviews with ELIfe participants and their team members.
With initiatives and consortiums around the world garnering significant grant money for lipidomics research, the field as a whole is poised to make an important contribution to the ever-increasing pool of knowledge about the role of lipids in human disease and metabolism. Interview with Fritz Spener and representatives of the US and Japanese Lipidomics Initiatives. Advertorial: Parliament Magazine, issue 210 of October 3, 2005, entitled "Fat is Bad?", stressing the need for financial support under FP7 for the area of metabolomics, and of lipidomics in particular. Survey: The data in the Lipidomics Expertise Platform database have been analyzed and the survey will be published on the website (see Annex 2 of the second periodic report). Other activities: - 2,500 scientists with an interest in lipids have been approached by e-mail in March and August 2006 with an invitation to attend the ELIfe general meeting. - Scientists outside the ELIfe consortium have been actively invited to take part in the ELIfe discussions on the development of lipidomics in a broader context. The "White Paper" on "Enabling Technologies for Studying the Genome, Proteome and Cytome of the Lipidome" has been made publicly available in an interactive format on the LEP website (http://www.lipidomics-expertise.de/). LEP-Wiki serves as the basis for defining areas within the lipidomics field where research is expected to have the largest impact for society, especially in the form of health benefits. - One issue is the prolongation of the European Lipidomics Initiative in the form of actual collaborations. A further result of the ELIfe SSA was the formation of a European consortium to submit in the first call of the FP7 a grant application for a large collaborative project (21 partners including 4 SMEs, coordinated by G. Schmitz, Regensburg), entitled 'Lipid droplets as dynamic organelles of fat deposition and release: Translational research towards human disease' (LipidomicNet). - Finally, the Eurocores theme proposal Euromembrane that was discussed at the first annual meeting has been adopted by ESF. Section 3 - Publishable results All papers have been published.  
LSSG-CT-2004-013032 ELIfe European Lipidomics Initiative: Shaping the Life Sciences Instrument: Specific Support Action Thematic Priority: FP6-2003-LIFESCIHEALTH-II; LSH-2003-3-6 TOWARDS A EUROPEAN LIPIDOMICS PROGRAMPlan for Using and Disseminating Knowledge (publishable version) Final Report 2005-2007 Period covered: from 1/1/05 to 1/7/07 Date of preparation: 1/1/08 Start date of project: 1/1/05 Duration: 2.5 years Project coordinator name: Prof. Gerrit van Meer Project coordinator organisation name: Utrecht University
Summary Over 2005 and 2006, the specific support action 'the European Lipidomics Initiative (ELIfe)' has resulted in four successful workshops where stakeholders from basic science, industry and medicine met to discuss cell biological, technological, industrial and clinical aspects of lipidomics. In addition, ELIfe contributed lipidomics sessions to four networking meetings, one on life sciences, one on the bioscience of lipids and two industrial lipid meetings. These workshops and meetings culminated in the concluding general meeting in October 2006, attended by a broad audience of 250 scientists. At the occasion of this meeting a special journal issue was published on 'Lipidome and Disease' [16]. The results of the the specific support action were reported in a series of policy papers in the scientific literature [4-6, 8-13], and a policy briefing on lipidomics and health of the European Science Foundation [14]. In addition, ELIfe contributed to a number of technical papers on lipid classification and data handling [1-3] and to a 500 page document entitled 'Enabling technologies for studying the genome, proteome and cytome of the lipidome.' [7]. This document will be presented on the Lipidomics Expertise Wiki Portal (LEP-Wiki): http://www-cgi.uni-regensburg.de/Klinik/Klinische_Chemie/lipidWiki/, to allow a direct interaction with the scientists in the field. Interviews with ELIfe members appeared in various journals [17,18]. A survey was prepared based on registrations in the Lipidomics Expertise Platform www.lipidomics-expertise.de with the purpose of identifying stakeholders and providing insight in the available expertise, which can be used for contacting specific centers for collaboration. A 260 page document entitled 'Lipid droplets and lamellar bodies as dynamic organelles connecting influx, efflux, and storage of lipids: Translational research towards human disease' was prepared as the basis for a grant proposal under FP7 by a number of ELIfe members plus other scientists. This proposal 'LipidomicNet' was recently selected for funding. A EuroCore theme proposal under the name EuroMembrane [15] has been accepted by the European Science Foundation and a call for applications is expected for early 2008. In summary, we believe that the European Lipidomics Initiative has created many opportunities for crossover between basic science and medical and commercial applications, and that it has inspired stakeholders to seek contact and establish strategic alliances. Because national funding agencies and policy makers value the European dimension, the project will impact on both the European and the national level in shaping policies and research activities, both in applied and fundamental research. One such field is that of nutrition and health. Technology development will allow more detailed analyses of lipid patterns in diseased and healthy persons, which will drive discussions with the food industry concerning the potential positive and negative effects of different types of (lipid) nutrition on human health with new health policies drawn up as a result. References [1.a] Fahy, E., S. Subramaniam, H.A. Brown, C.K. Glass, A.H. Merrill, Jr., R.C. Murphy, C.R. Raetz, D.W. Russell, Y. Seyama, W. Shaw, T. Shimizu, F. Spener, G. van Meer, M.S. Vannieuwenhze, S.H. White, J. Witztum, and E.A. Dennis (2005) A comprehensive classification system for lipids. J. Lipid Res. 46, 839-861. [1.b] idem: (2005) Eur. J. Lipid Sci. Technol. 107, 337-364 [2] Varfolomeyev, S., Efremenko, E., Beletskaya, I., Bertini, I., Blackburn, G.M., Bogdanov, A., Cunin, R., Eichler, J., Galaev, I., Gladyshev, V., O’Hagan, D., Haertle, T., Jarv, J., Karyakin, A., Kurochkin, I., Mikolajczyk, M., Poroikov, V., Sakharov, I., Spener, F., Voyer, N., and Wild, J. (2005) Postgenomic chemistry (IUPAC Technical Report). Pure Appl. Chem. 77, 1641–1654. [3] Spener F. (2005) Lipidomics and consequences: a new classification system for lipids. Eur. J. Lipid Sci. Technol. 107, 277-278. [4] van Meer, G. (2005) Cellular Lipidomics. EMBO J. 24, 3159-3165. [5] Schmitz, G., Liebisch, G., Langmann, T. (2006) Lipidomic strategies to study structural and functional defects of ABC-transporters in cellular lipid trafficking. FEBS Lett. 580, 5597-5610. [6] van Meer, G., Leeflang, B.R., Liebisch, G,. Schmitz, G., Goni, F.M. (2007) The European lipidomics initiative: enabling technologies. Methods Enzymol. 2007;432, 213-232. [7] White paper on 'Enabling technologies for studying the genome, proteome and cytome of the lipidome.' to be published in Wikipedia format on the LEP website. [8] Spener F. (2005) European Commission funds lipidomics project. Eur. J. Lipid Sci. Technol. 107, 1-2. [9] Griffiths, W. (2006) Why steroidomics in brain? Eur. J. Lipid Sci. Technol. 108, 707–708. [10] Helms, B. (2006) Host-Pathogen interactions: Lipids grease the way. Eur. J. Lipid Sci. Technol. 108, 895–897. [11] Spener, F., Kohlwein, S.D., and Schmitz, G. (2006) Lipid droplets and lamellar bodies – from innocent bystanders to prime targets of lipid research for combating human diseases. Eur. J. Lipid Sci. Technol. 108, 541-543. [12] Spener, F., Zechner, R., and Borlak, J. (2006) Is lipotoxicity an oxymoron? Eur. J. Lipid Sci. Technol. 108, 625-627. [13] van Meer, G. (2006) How do sphingolipids and lipid rafts relate to pathology? Eur. J. Lipid Sci. Technol. 108, 799–801. [14] van Meer, G. and Spener, F. (Co-Chairs), Leeflang, B.R. (Secretary), Beisiegel, U., Bougnoux, P., Goñi, F., Griffiths, W., Hartmann, T., Helms, B., Hoekstra, D., Julià-Sapé, M., Larijani, B., Moschetta, A., Mouritsen, O.G., Norata, G.D., Payrastre, B., Record, M., Schmitz, G., Simons, K., Tselepis, A., Vaz, W., Vigh, L., Voelker, D.R., Wakelam, M.J.O., and Wanders, R.J.A. (2008) Structural Medicine II: the Importance of Lipidomics for Health and Disease, European Science Foundation Policy Briefing, in press. [15] van Meer, G. (main proposer), Malhotra, V., Marsh, M., Simons, K., van der Goot, G., Warren, G. (2008) Membrane Architecture and Dynamics (EuroMEMBRANE), EuroCORE theme proposal. Call to be launched in spring 2008. [16] Helms, B. and van Meer, G., eds. (2006) Lipidome and Disease. FEBS Letters Special Issue. FEBS Lett. 580, 5429-5610. [17] Winckler, L. (2005) Lipidomics. Laborjournal 12, 20-23. [18] Hillyer, C.D. (2006) Lipidomics: taking it one lipid at a time. Inform 17, 206-208.
ELIfe flyer Advertorial in the Parliament Magazine, issue 210 of October 3, 2005, entitled "Fat is Bad?"
The data in the Lipidomics Expertise Platform database have been analyzed and the survey will be published on the website (see Annex 2 of the reports).
LSSG-CT-2004-013032 ELIfe European Lipidomics Initiative: Shaping the Life Sciences Instrument: Specific Support Action Thematic Priority: FP6-2003-LIFESCIHEALTH-II; LSH-2003-3-6 TOWARDS A EUROPEAN LIPIDOMICS PROGRAMAppendix 13 Science and society reporting questionnaire Yüklə 2,18 Mb. Dostları ilə paylaş:
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