Final Report Summary - GENPRO (Enhancing BSRC Al. Fleming research potential in genomics and proteomics applications)
Executive Summary:
a) Summary of aims
The aim of this project was to reinforce and enhance the scientific research potential of the BSRC Al. Fleming in the areas of functional genomics and proteomics. The main activities of the program included: i. Upgrading BSRC Al. Fleming's genomics and proteomics facilities; ii, Recruitment of experienced researchers and repatriation of a high-profile Greek scientist; iii, Developing strategic partnerships with centres of excellence in genomics and proteomics field; iv, Organisation of Workshops to facilitate transfer of knowledge at regional and international level. At the conclusion of the program all of the activities have been successfully completed and produced several significant achievements.
b) Work performed and main results
During the lifetime of the project we achieved all main objectives. These include:
1. Setting up management and Advisory Committees.
2. Recruitment of new personnel. Purchasing and Installation of new equipment (ABI SOLID4 High-throughput Sequencer and Thermo Scientific Orbitrap XL Mass Spectrometer).
3. Instruments' test runs have been performed.
4. A large number of runs with experimental samples have been performed, evaluated, some already reached the stage of scientific publication.
5. Quality controls of experiments have been routinely evaluated.
6. Project web site and intranet server has been constructed and established.
7. Short-term training visits to Mentor labs have been completed.
8. Workshop on Proteomics applications has been organised.
9. Workshop on Genomics applications has been organised.
10. The members of the consortium have participated in several international conferences, where data obtained by the instruments of the new facilities were presented.
11. Data from the new facilities were part of 28 publications in scientific journals.
12. The program contributed to one patent application.
c) Main benefits and impact
Among the major expected impacts of the program, several important results demonstrate the importance of the project. Briefly:
1. Quality of research at BSRC Al. Fleming has increased as the new instruments allow the execution of high throughput experiments that were not possible before.
2. The human potential of BSRC Al. Fleming has been improved by hiring 6 new experienced researchers, experts in the field of genomics and proteomics.
3. Integration of BSRC Al. Fleming into the European Research Area has been enhanced via establishing contacts with Mentor labs and other leading scientists in main international centers.
4. BSRC Al. Fleming's potential to attract new research funding was enhanced as evidenced by 9 successful Greek applications, 1 successful ERC Advanced and 1 ERC Consolidator grant application. The projects of these applications rely on using high throughput genomics and proteomics approaches.
5. The new genomics facility represents the basis of a novel initiative that aims at networking Greek genomics labs. Funding for this has already been obtained through a new Greek grant from the Greek General Secretary of Science and Technology (grant number: 09SYN-13-901).
6. The new genomics and proteomics facility has started to provide various sequencing and protein analysis services also to researchers outside of the Fleming Institute.
Project Context and Objectives:
Project context and objectives
The aim of this project was to reinforce and enhance the scientific research potential of the BSRC Al. Fleming in the areas of functional genomics and proteomics. Main focus was on strengthening the institute's capacities by setting up and operating facilities using next generation high-throughput technologies. The specific objectives of the project were:
1. Expansion of capabilities of genomics and proteomics research at BSRC Al. Fleming by the acquisition of new equipment.
2. Recruitment of incoming researchers with expertise in new-generation genomics and proteomics technologies and repatriation of an established Greek scientist.
3. Exchange of know-how and experience in new-generation genomics and proteomics approaches through twinning with Mentor Labs in EU's developed regions.
4. Development of strategic partnerships with centers of excellence in Europe.
5. Disseminating and promoting knowledge in genomics and proteomics science at local, regional and international level.
Four parallel actions were made to achieve these goals. These included:
1. Upgrading the Center's Genomics and Proteomics Facilities by purchasing next generation DNA sequencing platform and mass-spectrometer.
2. Recruitment of experienced researchers and repatriation of a high-profile Greek scientist.
3. Developing strategic partnerships with centers of excellence in genomics and proteomics field.
4. Organisation of Workshops to facilitate transfer of knowledge at regional and international level.
The project was planned to run for 36 months and anticipated to result in substantial development of BSRC Al. Fleming's potentials. It was also anticipated that the new upgraded facilities will be able to provide high quality sequencing and proteomics services for Greek scientists and possibly to scientists in the larger Mediterranean region. Through the dissemination activities of the program it was expected that GENPRO will provide vital forums for scientists in the field of Systems Biology and contribute to training activities in genomics and proteomics applications.
Project Results:
Work performed and major achievements
Workpackage 1: Installation/functioning of equipment and recruitment of ERT
The key goal of this WP was to upgrade BSRC Genomics and Proteomics facilities by purchasing and installation of a high-throughput next-generation sequencing instrument, a high-throughput high-resolution mass-spectrometer and the recruitment and training of technical personnel who will run these instruments. For the instruments public tenders were announced in February 2010. After evaluations of the offers an ABI SOLID4 sequencing instrument was purchased in 31st May 2010. This corresponded to a 3 months delay compared to the planned date.
A more significant delay in the acquisition of the second instrument (mass-spectrometer) occurred, due to the vendor's financial offer with higher price than that allowed in the tender. Because of legal restrictions we could not proceed and announced a new tender. Eventually, an Orbitrap XL instrument was purchased in 29th November 2010 (corresponds to 9 months delay).
We made effort to reduce the impact of the delayed purchase of the mass-spectrometer by pursuing extensive training in Mentor ML3 laboratory. While at the mid-term a request for "no cost extension" of the program seemed necessary, eventually the increased efforts invested after the period of November 2010 paid off and all major goals were achieved as planned within the funding period.
Initial testing and quality controls have been performed. These trials were successful. Additional preliminary experiments demonstrated the flawless functioning of both instruments. These included one ChIP-seq assay using CEBPa antibody on liver chromatin and one protein identification assay in immunoprecipitated material. Specific emphasis was given to establish computational support to link the instruments into the computer network of BSRC Al. Fleming.
Recruitment of 2 ERTs (Experienced Research Technicians) was realized in the first month of the project. ERT positions are not funded by the GENPRO program. The persons hired (Dr Martina Samiotaki and Dr Anna Haroniti) were engaged in the facilities at both, the instrument setup and full operation periods. Deliverables of this WP are D1-1, D1-2, D1-3 and D1-4. They have been achieved fully.
Workpackage 2: Recruitment of ERs and their integration into GENPRO's scientific activities
The objective of this workpackage is to enhance BSRC Al. Fleming's research potential in the area of genomics and proteomics through recruitment of high quality experts in the field. Open positions were first announced in 2009. The Management Committee of GENPRO the selected the following people:
ER2 Dr Vagelis Harokopos (Expert in Genomics applications. Nationality: Greek). Started in month 1.
ER3 Dr Martin Reczko (Expert Bioinformatician. Nationality: German) Started in month 1.
ER4 Dr Wolf Oerhl (Expert in Proteomics. Nationality: German). Started in month 1.
New announcements were published in May and June of 2010. Two scientists were selected:
ER1 Dr Pantelis Hatzis (Expert in Genomics applications. Nationality: Greek). Started in month 10.
ER5 Dr Mouratos Marios (Expert in Computational Biology. Nationality: Greek). Started in month 13. Due to family reasons Dr Mouratos left the position in April 2012. He was replaced by Dr Alexandros Dimopoulos (Expert in Bioinformatics. Nationality Greek).
hER - Repatriation of Mentor Lab 1, Dr Ragoussis Jiannis (hER) has been realised in month 13 as scheduled in the contract. From the beginning of the hiring ERs have been engaged in different projects using the new instruments. These included:
a. Studying epigenomes and transcriptomes.
b. Studying chromatin modifications.
c. Predicting and analysing microRNA targets.
d. Applying systems biology approaches in studying pathogenic signalling pathways.
e. Applying proteomics approaches to identify novel protein modifications and protein complex components.
The ERs work also included developing new and improving existing techniques employed in high throughput DNA sequencing and proteomics projects. Of particular importance is the building up of novel pipelines of algorithms and computer programs for various HTP sequencing applications like ChIPseq, RNAseq.
Another evidence for the enhancment of BSRC Al. Fleming research potential are the development and use of novel algorithms that has been made publicly available. These are:
1. DIANA-microT 3.0 an algorithm based on several parameters calculated individually for each microRNA and it combines conserved and non-conserved microRNA recognition elements into a final prediction score.
2. DIANA-mirExTra an algorithm that can identify microRNA effects to the Expression levels of protein-coding Transcripts, based on the frequency of six nucleotide long motifs (hexamers) in the 3'UTR sequences of genes.
3. DIANA-mirPath a web-based computational tool developed to identify molecular pathways potentially altered by the expression of single or multiple microRNAs.
4. TarBase5.0 the largest available manually curated target database, indexing more than 65,000 miRNA-gene interactions.
Between February 2010 and December 2012, these sites have been visited 272 500 times from all over the world demonstrating their quality and usefulness for the field of transcriptomics and epigenetics. Deliverable D2 (Report on full functioning of genomics and proteomics facility in research projects), has been achieved. This deliverable shows that after successful installation, the new instruments have started operation in real experiments and currently are in a routine use. It is also important to emphasise that in the short time period (3 years), the positive effects of the program in enhancing the research potential of BSRC Fleming are already evident as several scientific publications, some of them in very high impact journals (Science, PNAS, Mol Cell, J Cell Biol) were supported by the upgraded facilities. Publications so far publishing experiments using the facilities are listed in D2 and can also been found in GENPRO web site:
http://www.fleming.gr/en/investigators/Talianidis/genpro_publications.html
The facilities are now able to provide services in the following applications:
Genomics facility:
- FAIRE-seq (Formaldehyde Assisted Identificanton of Regulatory Elements)
- ChIP-seq (Chromatin Immunoprecipitation)
- RNA-seq (RNA sequencing)
- miRNA-seq (micro RNA sequencing)
- PAR-CLIP-seq (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immuno-precipitation)
- Whole exome sequencing
- Whole genome sequencing
Proteomics facility:
- Label free quantification (LFQ) 8 projects
- Stable isotopic labelling - 10 projects
- Reporter ion quantification - 9 projects
- Protein MW determination and multumerisation - 12 projects
- Protein posttranslational modification detection - 14 projects
The proteomics facility was also engaged in technology improvement activities that resulted in:
1. Advanced sample preparation methods for protein digestion.
2. Advanced peptide separation and data analysis methods.
Workpackage 3: Twinning collaborations with Mentor Labs and transfer of knowledge
This workpackage had two objectives: Transfer of knowledge from top genomics and proteomics centres and the establishment of collaborative links with leading researchers in the field of genomics and proteomics. The key instrument to achieve these goals was twinning collaborations with Mentor labs. Contacts with the 4 Mentor labs have been made at the onset of the program and some collaborations with them have been initiated.
The Mentor labs of the project are:
1. Wellcome Trust Center for Human Genetics, University of Oxford, UK web site: http://www.well.ox.ac.uk/genomics/index.shtml
Contact person: Jiannis Ragoussis
2. Max Delbruck Center for Molecular Medicine, Berlin, Germany
web site: http://www.mdc-berlin.de/en/research/research_teams
Contact person: Nikolaus Rajewsky
3. Ludwig Maximilians University (LMU), Munich, Germany
web site: http://proteinanalytik.web.med.uni-muenchen.de
Contact person: Axel Imhof
4. Centre for Molecular and Cellular Physiology, University of Oxford, UK
web site: http://www.ndm.ox.ac.uk/researcher/benedikt-kessler
Contact person: Benedict Kessler
An essential element of collaborations and transfer of knowledge is the short-term visits of GENPRO members to Mentor Labs. During the reporting period eleven short-term visits to Mentor Labs have been realised.
The participants were engaged in:
1. Project planning, discussions about the Organisation of facilities, presentations of previous and current projects in Fleming labs and discussions about future joint grant applications.
2. Training in genomics and proteomics applications, performing experiments to set up collaborative projects, developing new computational tools for HTP genomics applications.
The objectives of this work package have been successfully executed. There was an extensive transfer of knowledge from MLs, which helped to acquire the know-how running the highly specialised and complex sequencing instrument and the mass spectrometer. As a result of the efficient knowledge transfer, the two facilities very quickly established the various sequencing and protein analysis technologies described above in WP2. In fact, within of about a year of operation the facilities were in position to offer high quality services in several different applications.
Mentor Lab 1 (Jiannis Ragoussis at Oxford University, UK) stopped functioning as Mentor Lab after the first year and joined BSRC Al. Fleming as member of GENPRO. At the same time Dr Ragoussis took charge of Fleming's Genomics facility. As described in Deliverable D3-2 two collaborations with Mentor Labs on future EU projects have been initiated.
Workpackage 4: Organisation of Workshops and Dissemination activities
This Workpackage had 4 objectives: Organisation of workshops, construction of web site, Organisation of seminar series at Fleming and presentations of GENPRO activities in conferences.
Workshop 1, "Workshop on Functional and Structural Proteomics" was organised with about 5 months delay on month 23 of the program.
Workshop 2, "Next generation sequencing methods and applications" were organised as planned in month 24 of the program.
They were advertised in GENPRO web site, in BSRC Al. Fleming web site, the web sites of major Greek universities and research centers, the web sites of two EU-ITN programs (DISCHROM and INTEGER) and through e-mailing to about 400 Greek and European biology labs.
As described in Deliverables 4-1 and 4-2 both workshops consisted a seminar / presentation part and a practical hands-on course in the facilities of BSRC Al. Fleming. The presentation part of the Proteomics workshop was co-organised with PROFI (Regpot program in IMBB-FORTH, Crete) and Dischrom (Marie Curie ITN program at Fleming). Both workshops attracted large audience: 89 and 120 people for Workshop 1 and Workshop 2, respectively. For the practical courses 12 and 20 students were selected. Some of the related activities included studies with animals. All of the activities of the program were in compliance with the ethical standards and requirements of the ethical review accompanying the contract.
Potential Impact:
GENPRO web site was constructed in the first month of the project. The web site can be accessed at: http://www.fleming.gr/en/investigators/Talianidis/genpro_overview.html
It contains the main information about the project including overview of the activities, personnel data, Mentor lab data, description of facilities, vacancies, workshop schedules and programs and scientific publications. The web site has been regularly updated by the coordinator. An important dissemination activity is the GENPRO initiative to organize publicly open seminar series at BSRC Fleming premises, by inviting external speakers from different biological fields. The thematic program had a common feature: emphasis on global analysis using modern genomics and proteomics approaches. The following invited seminars were organised:
2010-22-4 Ancient animal miRNAs and the evolution of tissue identity Dr Fay Christodoulou EMBL, Germany.
2010-27-5 Transgenerational Epigenetic Inheritance in Colliding Genomes and Dividing Cells Antonis Giakountis, Ph.D RNA silencing and Epigenetics, University of Cambridge, England.
2010-31-5 Cytokine signaling in inflammatory bowel diseases Prof. Markus Neurath Universit Asklinikum Erlangen.
2010-2-7 A discussion on Epigenetics Professor Emeritus Constantine Moiras University of Medicine of Athens.
2010-10-9 Lgr5 adult stem cells in tissue renewal and disease Nick Barker, Ph.D. Hubrecht Laboratory, Netherlands Institute of Developmental Biology.
2010-14-10 Transcription factor networks & long range interactions Professor Frank Grosveld Erasmus Medical Center, Rotterdam, The Netherlands.
2010-20-12 Drosophila models of human infections & carcinogenesis Dr Georgios Apidianakis Department of Surgery & Molecular Biology Harvard Medical School.
2011-28-01 Maping RNA-protein interactions in translation Dr. Yiota Kafasla Department of Biochemistry, Un. of Cambridge, UK.
2011-18-03 Regulation of immune responses by IKK-induced NF-kB1 p105 proteolysis Dr Steve Ley MRC-NIMR, London, UK.
2011-10-05 The Integrated Stress Response in Tumorigenesis: Problems and Opportunities for Therapeutic Intervention Costas Koumenis, Associate Professor Department Radiation Oncology, University of Pennsylvania, School of Medicine.
2011-11-05 RANKL and Osteoimmunology, Prof Hiroshi Takayanagi, Cell Signalling Department, Tokyo Medical and Dental University
2011-14-07 Id3 restricts the generation of thymic innate-like T lymphocytes, Dr Mihalis Verykokakis, Dept of Pathology & Committee on Immunology, University of Chicago.
2011-13-09 Leukaemia Stem Cells in Acute Myeloid Leukaemia, Dr Paresh Vyas, MRC Molecular Haematology Unit Weatherall Institute for Molecular Medicine Oxford, UK.
2011-10-10 Induced glioma-initiating cell models reveal new therapeutic targets, Dr Toru Kondo, Dept of Stem Cell Biology, Ehime University Proteo-Medicine Research Center, Japan.
2011-01-11 Macrophage inflammation and chemotaxis in mouse models of atherosclerosis, Dr Pieter Goossens, Cardiovascular Research Institute of Maastricht.
2012-19-04 Epigenetic control of the mobile genome: implications for cell identity and disease, Dr Valerio Orlando, Dulbecco Telethon Institute, IRCCS Fondazione Santa Lucia, Rome - Italy.
2012-19-10 Regulation of macrophage polarization By Akt kinases and miRNAs, Dr Christos Tsatsanis, Dpt. of Clinical Chemistry, School of Medicine, University of Crete. The above seminars attracted audiences between 80-120 people, represented about equally by scientists from BSRC Fleming and scientists from other institutions of Greece, mainly from Athens.
Another important dissemination activity is the construction, curation and open access availability of web resources for computational models in systems biology. This is based on computational tools developed by GENPRO members. The DIANA (Dna Intelligent analysis) site can be accessed at: http://diana.cslab.ece.ntua.gr/
In addition, work performed using GENPRO facilities have been highlighted in audio podcast interview by M. Fousteri:
Biobytes, February 7, 2011 Journal of Cell Biology, The Rockefeller University Press. Online, audio podcast on the regulation of Nucleotide Excision DNA Repair (Overmeer et al., 2011).
GENPRO members have also published 28 scientific papers in which the facilities were used. These publications are listed in Deliverable D2 and also in the web site of GENPRO:
http://www.fleming.gr/en/investigators/Talianidis/genpro_publications.html
Below is a selection of representative publications:
Koliaraki V, Roulis M, Kollias G. 2012, "Tpl2 regulates intestinal myofibroblast HGF release to suppress colitis-associated tumorigenesis.", J Clin Invest. 122:4231-42.
Nikolaou K., Tsagaratou A., Eftychi C., Kollias G., Mosialos G., Talianidis I . 2012, "Inactivation of the deubiquitinase CYLD in hepatocytes causes apoptosis, inflammation, fibrosis and cancer.", Cancer Cell, 21: , 738-750.
Reczko M, Maragkakis M, Alexiou P, Papadopoulos GL, Hatzigeorgiou AG. 2012, "Accurate microRNA Target Prediction Using Detailed Binding Site Accessibility and Machine Learning on Proteomics Data.", Front Genet. 2011;2:103. 2011;2:103.
Yiakouvaki A, Dimitriou M, Karakasiliotis I, Eftychi C, Theocharis S, Kontoyiannis DL 2012, "Myeloid cell expression of the RNA-binding protein HuR protects mice from pathologic inflammation and colorectal carcinogenesis.", J Clin Invest. 122(1):48-61.
Gkiafi Z, Panayotou G. 2011, "Comparative Proteomic Analysis Implicates COMMD Proteins as Epstein-Barr Virus Targets in the BL41 Burkitt's Lymphoma Cell Line.", J Proteome Res. , 10:2959-68.
Schmidt D, Wilson MD, Ballester B, Schwalie PC, Brown GD, Marshall A, Kutter C, Watt S, Martinez-Jimenez CP, Mackay S, Talianidis I, Flicek P, Odom DT. 2010, "Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding." Science. 328(5981):1036-40.
Results from the Genomics services of GENPRO also contributed the filing of one patent application:
TNF superfamily trimerization inhibitors, Inventors: Georgios Kollias, Eleni Douni
Application Number: P95195PC00. Priority Date: 12 August 2011.
A very important activity of GENPRO members during the reporting period is the participation in scientific study groups disseminating new knowledge gained by emerging high throughput genomics and proteomics technologies. Dr George Kollias is the Coordinator of the Study Group on Animal Models (SGAM) funded by the European League Against Arthritis (EULAR). The aim of EULAR SGAM was to draft a guidance document to provide recommendations on current bottlenecks and limitations in predictive animal modelling and to guide future directions that will enhance innovation in arthritis pre-clinical research. The Study Group met at the EULAR House in Zurich, Switzerland, on March 18th and 19th 2010 and the guidance document was published on April 24, 2011 in the Annals of Rheumatic Diseases. See link: http://www.ncbi.nlm.nih.gov/pubmed/21628308.
The use of emerging technologies in -omics profiling (including chromatin structure, epigenetic, miRNA, transcriptional, post-transcriptional and proteomic analysis), to facilitate the alignment of mouse models to human disease, is a key point in the document, which concludes that "the association of phenotypes to molecular profiles (gene, protein and metabolite expression) offers an invaluable tool for unveiling pathogenic mechanisms, pathways and targets and also for discovering predictive biomarkers for diagnosis and treatment."
Finally, GENPRO members presented their related work in several international conferences. Major presentations during the reporting period were as follows:
Iannis Talianidis, Epigenetic mechanisms regulating liver development, metabolism and disease, XXIV International Complement Workshop. Chania, Oct 10-15. 2012. ~300 participants.
Iannis Talianidis, Epigenetic mechanisms regulating liver development, metabolism and disease, Epigenetics Conference Budapest, Hungary Sept 20-22. 2012 ~150 participants.
Kostas Nikolaou, Panagiotis Moulos, George Chalepakis, Hisanobu Oda, Danny Reinberg and Iannis Talianidis, PR-Set7-mediated H4K20 methylation controls genome integrity and metabolic pathways in liver. 10th EMBL Conference in Transcription and Chromatin Heidelberg Aug. 25-28. 2012 ~300 participants.
Samiotaki, M. "Analysis of protein-protein interactions: quantitave proteomic strategies". 2nd Greek Orbitrap User Meeting. Crete, Greece. 23-24 April 2012. ~40 participants.
Vlachonasios K, Poulios S, Topouzis S, Samiotaki M and Panayotou G, Synergistic action of histone acetyltransferase GCN5 and CLAVATA1 receptor kinase negatively affect ethylene responses. 23rd International Conference on Arabidopsis Research, Vienna, Austria, July 3-7, 2012. ~200 participants.
Oehrl W., Cotsiki M., Samiotaki M. and Panayotou G. Regulatory role of the M3/6 dual-specificity phosphatase in JNK signalling. 37th FEBS & 22nd IUBMB Congress, Sevilla 4-9 September 2012. ~150 section participants.
Samiotaki, M. Recent advances in pharmacoproteomics. 1st Conference of Pharmaceutical Sciences, Athens, Greece. 27-30 April 2012. ~100 participants.
Aidinis V. Autotaxin and LPA signalling in the pathogenesis of chronic inflammatory diseases 2011 FASEB Summer Research Conference Lysophospholipid mediators in health and disease. August 14-19, Lucca, Italy. (2011). ~120 participants.
V.S. Gartaganis, M. Samiotaki, G. Panayotou, S.P. Gartaganis. Proteomic analysis of aqueous humour from patients with Pseudoexfoliation syndrome. SOE Congress, Geneva, 5-7 June 2011. ~200 participants.
Ioannis Pandis, Caroline Ospelt, Niki Karagianni Maria Denis, Martin Reczko,Carme Camps, Artemis Hatzigeorgiou, Jiannis Ragoussis, Steffen Gay and George Kollias. Association of microRNA-221/222 and -323-3p with rheumatoid arthritis via predictions using the human TNF transgenic mouse model. 8th Global Arthritis Research Network (GARN) Meeting, November 14-16, 2011. ~200 participants.
Maria Fousteri. Genome wide approaches in DNA repair. ICGC Meeting in Epigenetics and non-coding RNAs. Amsterdam Nov 6-10. 2011. ~100 participants.
Iannis Talianidis. Operation of a transcription factor network driving liver development. 9th International Conference on Pathways, Networks, and Systems Medicine. Aegean Conferences Chania, June 10-15. 2011 ~200 participants.
Ikonomou G., Kostourou V., Landegren U., Soderberg O., Samiotaki M., Panayotou G. Interplay between oncogenic K-ras and wild type H-ras in colorectal cancer. EMBO Conference Series "SPATIAL 2011", 15-19 May 2011, Engelberg, Switzerland, ~ 100 participants.
V. Aidinis. Autotaxin and Phospholipid signalling in Chronic Inflammation. - Advances in Immunology and Cancer Biology workshop. 15-17 April 2011, Bogazici University, Istanbul, Turkey. ~ 150 participants.
Fousteri M. Deciphering the role of transcription and chromatin remodelling in DNA repair. Conference on Responses to DNA damage: from molecular mechanisms to human disease. Egmond aan Zee, The Netherlands, April 3-8, 2011. Approx. 350-400 participants.
Ikonomou G., Samiotaki M., Kostourou V., Pintzas A., Panayotou G. Interplay between oncogenic K-ras and wild type H-ras in Caco2 cell transformation. 61st Meeting of Hellenic Society of Biochemistry & Molecular Biology, 15-17 October 2010, Alexandroupoli, Greece. 400 participants.
Nikolaou K. and Talianidis I. CYLD inactivation in liver. 61st Meeting of Hellenic Society of Biochemistry & Molecular Biology, 15-17 October 2010, Alexandroupoli, Greece. 400 participants.
M. Karagiannopoulos, M. Samiotaki, G. Panayotou, ME. Lekka. Effect of propanil and diazinon on the protein profile of Tetrahymena. - 1st International Proteomics Conference on Crete-IPCC01. Crete, Greece. 7 and 8 October 2010. ~100 participants.
M. Samiotaki, M. Panopoulou, G. Panayotou, A. Ikonomidis. RNase-mediated post-transcriptional regulation of gene ompA seems to be the major mechanism of carbapenem heteroresistance in A. baumannii. ECCMID-2011. 21st European Congress of Clinical Microbiology and Infectious Diseases. Milan, Italy 7-10 May 2011. ~250 participants.
Samiotaki M and Panayotou G. 1st Greek Orbitrap User Meeting. Crete,Greece. 9th October 2010. ~30 participants.
G. Kollias. The pros and cons of interfering with TNF-dependent functions. The Second Kitasato Symposium: New Prospects for Cytokines, Palais am Festungsgraben, Berlin, Germany May 27-29, 2010 ~ 150 participants.
G. Kollias. Tumour necrosis factor and inflammatory disease. Mouse models for human diseases. The Royal Society London, UK, May 19-21 2010 ~ 150 participants.
I. Talianidis. Lysine methylation regulates E2F1-induced cell death. 9th EMBL Conference on Transcription and Chromatin. Heidelberg August 28-31. 2010 ~300 participants.
Iannis Talianidis. Transcription Regulation in Liver. FASEB Summer Research Conference, Liver Growth, Injury and Metabolism: Basic and Applied Biology, Snowmass Village, Colorado August 15-20, 2010 ~ 300 participants.
Workpackage 5: Evaluation and Management
The objectives of Workpackage 5 (Evaluation and Management) are:
a. Setting up the Management and Advisory Committee.
b. Monitoring the implementation of the program and reporting achievements.
c. Evaluation of the success of the program.
The Management Committee was set up at the start of the project. It is composed of the GENPRO Researchers (Aidinis V., Fousteri M., Hatzigeorgiou A., Kollias G., Kontoyannis D., Panayotou G., Strouboulis J.). During its first unofficial meeting in November 2009, it specified the composition of the Advisory Committee, which was approved in the first official Management and Advisory Committee meeting in December 2. 2009 at BSRC Fleming. The Advisory Committee is composed of the heads of the Mentor Labs (Jiannis Ragoussis, Benedikt Kessler, Axel Imhof and Nikolaus Rajewsky).
The Management Committee has met 5 more times during the duration of the project:
In April 22. 2010, in October 12. 2010, in March 11. 2011, in January 10. 2012 and in November 12. 2012. All meetings were at the premises of BSRC Al. Fleming.
In the first Management Committee meeting held together with the Advisory Committee, discussions and decisions were made on the following issues:
1. Hiring new personnel.
2. Specifications of desired DNA sequencer and Mass Spectrometer.
3. Timetables and Deliverables of the project.
In the subsequent Management Committee meetings discussions and decisions were made on:
1. Administrative matters related to tenders and job contracts.
2. Room assignments and Organisation of facilities.
3. Scientific projects using the equipment in the new facilities.
4. Organisation of workshops.
5. Web sites and Organisations.
6. Seminar series at Fleming.
In the last Management Committee meeting (Nov. 2012) was also attended by ML2 and ML3. In this meeting the achievements of the project were evaluated and plans for the possibilities of future expansion, upgrades were discussed.
Summary of the major decisions made on interim Management Meetings:
1. Selection of 3 scientists hired by GENPRO in the first round (Dec. 1 2009).
2. Purchase of ABI-SOLID4 DNA sequencing platform.
3. Purchase of Orbitrap-XL mass-spectrometer.
4. Approval of GENPRO Web-site content.
5. Assignment of new rooms for the instruments, expansion of the areas of the existing facilities.
6. Approval of 4 short-term visits to Mentor labs.
7. Approval of invited speakers for Fleming Seminars.
8. Tentative plans for Workshop 1 and Workshop 2.
9. Decision of postponing Workshop 1 to October 6. 2011.
10. Operation plan for the facilities to allow the use by external scientist.
11. Selection of 2 scientists hired by GENPRO in the second round of announcement (Sept. and Dec. 1 2010).
12. Final Workshop programs and sending invitations.
13. Approvals of additional visits to MLs and participation in conferences.
14. Decision of replacing Dr Mouratos with Dr Dimopoulos for the last period of the program.
15. Decision of extending Service Contracts for the instruments by one year payable from other sources.
16. Approval of the list of services provided by the two units to external users.
In the last meeting (November 2012) the Management Committee reviewed the status and the progress of the project and provided the overall assessment shown below:
Overall Assessment
After the first assessment in March 2011, significant progress has been made. Combined with the first period's conclusions, the GENPRO project significantly contributed to enhancing the research potential of BSRC Al. Fleming:
a. The project provided new state of the art instrumentations for the Genomics and Proteomics facility of BSRC Al. Fleming. The facilities are equipped with the most modern instrumentation. This allows performing frontier research at the institute.
b. The project contributed to the improvement of BSRC Research potential by making it possible to hire highly qualified Experienced Researchers and repatriate an established Greek scientist.
c. The project aided the development of new contacts with scientists working in leading centers of Europe.
The overall progress of the project was high. All of the deliverables have been achieved. The main points concerning the progress of the project are:
Goals achieved:
a. Purchased and installed ABI SOLID4 High-throughput Sequencer.
b. Purchased and installed Thermo Scientific Orbitrap XL Mass Spectrometer.
c. Hiring of high quality personnel with expertise specified in the contract has been completed.
d. Repatriation of hER has been achieved.
e. Training of personnel has been completed.
f. Instruments test runs have been performed and first tests with experimental samples have been run. Data were collected and quality controls have been evaluated.
g. Instruments have run several experimental samples.
h. Several experimental approaches have been set-up and used routinely.
i. The facilities reached the level to provide services for outside users in several sequencing and proteomics applications.
j. Twinning collaborations with Mentor labs have been initiated.
k. Web site has been constructed and several other means of dissemination (other web tools, webinar, scientific publications, conference presentations and participation in study groups) have been successfully realised.
Deviations from the original plan:
a. Significant delay in the purchase of the instruments (DNA sequencer and Mass-spectrometer).
b. Postponement of Workshop-1 by 5 months.
Despite the above delays Workshop-1 was organised with success. The delay of instrument purchase eventually did not affect the implementation of the goals. The success of the program was also evident by the number of new competitive grant applications from GENPRO members that were successful for funding. New grants in which the proposed topics require the existence of an in house Genomics or Proteomics facility are:
5 Greek grants (Aristeia and Synergasia program)
3 Greek grants (ESPA Post-doctoral program)
1 Greek grant (Thales program)
1 ERC Advanced Investigator Award
1 ERC Consolidator Award.
GENPRO members have also submitted 5 independent applications for the Marie Curie ITN and HEALTH program, which are currently being evaluated. Furthermore the new genomics facility represents the basis of a novel initiative that aims at networking Greek genomics labs. Funding for this has been obtained from the Greek General Secretary of Science and Technology (grant number: 09SYN-13-901). Another very important development in BSRC Al. Fleming where the GENPRO facilities played pivotal role is the Center's participation in the ESFRI Infrastructure project, the European Infrastructure for phenotyping and archiving of model mammalian genomes. Greece, through the General Secretariat for Investments and Development, has recently committed 3,9 million Euros for the development of the Greek node of Infrafrontier, which is coordinated by BSRC Al. Fleming. Both the Genomics and Proteomics facilities will continue to support INFRAFRONTIER-GR, whose activities are described in http://www.fleming.gr/infrafrontier-GR/
Project website: http://www.fleming.gr/en/investigators/Talianidis/genpro_overview.html
Iannis Talianidis
BIOMEDICAL SCIENCES RESEARCH CENTER ALEXANDER FLEMING
34, Alexander Fleming Street, 16672 Vari, Athens, Greece.
Phone. +30 210 965 3773
Fax +30 210 9653934
e-mail talianidis@fleming.gr
a) Summary of aims
The aim of this project was to reinforce and enhance the scientific research potential of the BSRC Al. Fleming in the areas of functional genomics and proteomics. The main activities of the program included: i. Upgrading BSRC Al. Fleming's genomics and proteomics facilities; ii, Recruitment of experienced researchers and repatriation of a high-profile Greek scientist; iii, Developing strategic partnerships with centres of excellence in genomics and proteomics field; iv, Organisation of Workshops to facilitate transfer of knowledge at regional and international level. At the conclusion of the program all of the activities have been successfully completed and produced several significant achievements.
b) Work performed and main results
During the lifetime of the project we achieved all main objectives. These include:
1. Setting up management and Advisory Committees.
2. Recruitment of new personnel. Purchasing and Installation of new equipment (ABI SOLID4 High-throughput Sequencer and Thermo Scientific Orbitrap XL Mass Spectrometer).
3. Instruments' test runs have been performed.
4. A large number of runs with experimental samples have been performed, evaluated, some already reached the stage of scientific publication.
5. Quality controls of experiments have been routinely evaluated.
6. Project web site and intranet server has been constructed and established.
7. Short-term training visits to Mentor labs have been completed.
8. Workshop on Proteomics applications has been organised.
9. Workshop on Genomics applications has been organised.
10. The members of the consortium have participated in several international conferences, where data obtained by the instruments of the new facilities were presented.
11. Data from the new facilities were part of 28 publications in scientific journals.
12. The program contributed to one patent application.
c) Main benefits and impact
Among the major expected impacts of the program, several important results demonstrate the importance of the project. Briefly:
1. Quality of research at BSRC Al. Fleming has increased as the new instruments allow the execution of high throughput experiments that were not possible before.
2. The human potential of BSRC Al. Fleming has been improved by hiring 6 new experienced researchers, experts in the field of genomics and proteomics.
3. Integration of BSRC Al. Fleming into the European Research Area has been enhanced via establishing contacts with Mentor labs and other leading scientists in main international centers.
4. BSRC Al. Fleming's potential to attract new research funding was enhanced as evidenced by 9 successful Greek applications, 1 successful ERC Advanced and 1 ERC Consolidator grant application. The projects of these applications rely on using high throughput genomics and proteomics approaches.
5. The new genomics facility represents the basis of a novel initiative that aims at networking Greek genomics labs. Funding for this has already been obtained through a new Greek grant from the Greek General Secretary of Science and Technology (grant number: 09SYN-13-901).
6. The new genomics and proteomics facility has started to provide various sequencing and protein analysis services also to researchers outside of the Fleming Institute.
Project Context and Objectives:
Project context and objectives
The aim of this project was to reinforce and enhance the scientific research potential of the BSRC Al. Fleming in the areas of functional genomics and proteomics. Main focus was on strengthening the institute's capacities by setting up and operating facilities using next generation high-throughput technologies. The specific objectives of the project were:
1. Expansion of capabilities of genomics and proteomics research at BSRC Al. Fleming by the acquisition of new equipment.
2. Recruitment of incoming researchers with expertise in new-generation genomics and proteomics technologies and repatriation of an established Greek scientist.
3. Exchange of know-how and experience in new-generation genomics and proteomics approaches through twinning with Mentor Labs in EU's developed regions.
4. Development of strategic partnerships with centers of excellence in Europe.
5. Disseminating and promoting knowledge in genomics and proteomics science at local, regional and international level.
Four parallel actions were made to achieve these goals. These included:
1. Upgrading the Center's Genomics and Proteomics Facilities by purchasing next generation DNA sequencing platform and mass-spectrometer.
2. Recruitment of experienced researchers and repatriation of a high-profile Greek scientist.
3. Developing strategic partnerships with centers of excellence in genomics and proteomics field.
4. Organisation of Workshops to facilitate transfer of knowledge at regional and international level.
The project was planned to run for 36 months and anticipated to result in substantial development of BSRC Al. Fleming's potentials. It was also anticipated that the new upgraded facilities will be able to provide high quality sequencing and proteomics services for Greek scientists and possibly to scientists in the larger Mediterranean region. Through the dissemination activities of the program it was expected that GENPRO will provide vital forums for scientists in the field of Systems Biology and contribute to training activities in genomics and proteomics applications.
Project Results:
Work performed and major achievements
Workpackage 1: Installation/functioning of equipment and recruitment of ERT
The key goal of this WP was to upgrade BSRC Genomics and Proteomics facilities by purchasing and installation of a high-throughput next-generation sequencing instrument, a high-throughput high-resolution mass-spectrometer and the recruitment and training of technical personnel who will run these instruments. For the instruments public tenders were announced in February 2010. After evaluations of the offers an ABI SOLID4 sequencing instrument was purchased in 31st May 2010. This corresponded to a 3 months delay compared to the planned date.
A more significant delay in the acquisition of the second instrument (mass-spectrometer) occurred, due to the vendor's financial offer with higher price than that allowed in the tender. Because of legal restrictions we could not proceed and announced a new tender. Eventually, an Orbitrap XL instrument was purchased in 29th November 2010 (corresponds to 9 months delay).
We made effort to reduce the impact of the delayed purchase of the mass-spectrometer by pursuing extensive training in Mentor ML3 laboratory. While at the mid-term a request for "no cost extension" of the program seemed necessary, eventually the increased efforts invested after the period of November 2010 paid off and all major goals were achieved as planned within the funding period.
Initial testing and quality controls have been performed. These trials were successful. Additional preliminary experiments demonstrated the flawless functioning of both instruments. These included one ChIP-seq assay using CEBPa antibody on liver chromatin and one protein identification assay in immunoprecipitated material. Specific emphasis was given to establish computational support to link the instruments into the computer network of BSRC Al. Fleming.
Recruitment of 2 ERTs (Experienced Research Technicians) was realized in the first month of the project. ERT positions are not funded by the GENPRO program. The persons hired (Dr Martina Samiotaki and Dr Anna Haroniti) were engaged in the facilities at both, the instrument setup and full operation periods. Deliverables of this WP are D1-1, D1-2, D1-3 and D1-4. They have been achieved fully.
Workpackage 2: Recruitment of ERs and their integration into GENPRO's scientific activities
The objective of this workpackage is to enhance BSRC Al. Fleming's research potential in the area of genomics and proteomics through recruitment of high quality experts in the field. Open positions were first announced in 2009. The Management Committee of GENPRO the selected the following people:
ER2 Dr Vagelis Harokopos (Expert in Genomics applications. Nationality: Greek). Started in month 1.
ER3 Dr Martin Reczko (Expert Bioinformatician. Nationality: German) Started in month 1.
ER4 Dr Wolf Oerhl (Expert in Proteomics. Nationality: German). Started in month 1.
New announcements were published in May and June of 2010. Two scientists were selected:
ER1 Dr Pantelis Hatzis (Expert in Genomics applications. Nationality: Greek). Started in month 10.
ER5 Dr Mouratos Marios (Expert in Computational Biology. Nationality: Greek). Started in month 13. Due to family reasons Dr Mouratos left the position in April 2012. He was replaced by Dr Alexandros Dimopoulos (Expert in Bioinformatics. Nationality Greek).
hER - Repatriation of Mentor Lab 1, Dr Ragoussis Jiannis (hER) has been realised in month 13 as scheduled in the contract. From the beginning of the hiring ERs have been engaged in different projects using the new instruments. These included:
a. Studying epigenomes and transcriptomes.
b. Studying chromatin modifications.
c. Predicting and analysing microRNA targets.
d. Applying systems biology approaches in studying pathogenic signalling pathways.
e. Applying proteomics approaches to identify novel protein modifications and protein complex components.
The ERs work also included developing new and improving existing techniques employed in high throughput DNA sequencing and proteomics projects. Of particular importance is the building up of novel pipelines of algorithms and computer programs for various HTP sequencing applications like ChIPseq, RNAseq.
Another evidence for the enhancment of BSRC Al. Fleming research potential are the development and use of novel algorithms that has been made publicly available. These are:
1. DIANA-microT 3.0 an algorithm based on several parameters calculated individually for each microRNA and it combines conserved and non-conserved microRNA recognition elements into a final prediction score.
2. DIANA-mirExTra an algorithm that can identify microRNA effects to the Expression levels of protein-coding Transcripts, based on the frequency of six nucleotide long motifs (hexamers) in the 3'UTR sequences of genes.
3. DIANA-mirPath a web-based computational tool developed to identify molecular pathways potentially altered by the expression of single or multiple microRNAs.
4. TarBase5.0 the largest available manually curated target database, indexing more than 65,000 miRNA-gene interactions.
Between February 2010 and December 2012, these sites have been visited 272 500 times from all over the world demonstrating their quality and usefulness for the field of transcriptomics and epigenetics. Deliverable D2 (Report on full functioning of genomics and proteomics facility in research projects), has been achieved. This deliverable shows that after successful installation, the new instruments have started operation in real experiments and currently are in a routine use. It is also important to emphasise that in the short time period (3 years), the positive effects of the program in enhancing the research potential of BSRC Fleming are already evident as several scientific publications, some of them in very high impact journals (Science, PNAS, Mol Cell, J Cell Biol) were supported by the upgraded facilities. Publications so far publishing experiments using the facilities are listed in D2 and can also been found in GENPRO web site:
http://www.fleming.gr/en/investigators/Talianidis/genpro_publications.html
The facilities are now able to provide services in the following applications:
Genomics facility:
- FAIRE-seq (Formaldehyde Assisted Identificanton of Regulatory Elements)
- ChIP-seq (Chromatin Immunoprecipitation)
- RNA-seq (RNA sequencing)
- miRNA-seq (micro RNA sequencing)
- PAR-CLIP-seq (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immuno-precipitation)
- Whole exome sequencing
- Whole genome sequencing
Proteomics facility:
- Label free quantification (LFQ) 8 projects
- Stable isotopic labelling - 10 projects
- Reporter ion quantification - 9 projects
- Protein MW determination and multumerisation - 12 projects
- Protein posttranslational modification detection - 14 projects
The proteomics facility was also engaged in technology improvement activities that resulted in:
1. Advanced sample preparation methods for protein digestion.
2. Advanced peptide separation and data analysis methods.
Workpackage 3: Twinning collaborations with Mentor Labs and transfer of knowledge
This workpackage had two objectives: Transfer of knowledge from top genomics and proteomics centres and the establishment of collaborative links with leading researchers in the field of genomics and proteomics. The key instrument to achieve these goals was twinning collaborations with Mentor labs. Contacts with the 4 Mentor labs have been made at the onset of the program and some collaborations with them have been initiated.
The Mentor labs of the project are:
1. Wellcome Trust Center for Human Genetics, University of Oxford, UK web site: http://www.well.ox.ac.uk/genomics/index.shtml
Contact person: Jiannis Ragoussis
2. Max Delbruck Center for Molecular Medicine, Berlin, Germany
web site: http://www.mdc-berlin.de/en/research/research_teams
Contact person: Nikolaus Rajewsky
3. Ludwig Maximilians University (LMU), Munich, Germany
web site: http://proteinanalytik.web.med.uni-muenchen.de
Contact person: Axel Imhof
4. Centre for Molecular and Cellular Physiology, University of Oxford, UK
web site: http://www.ndm.ox.ac.uk/researcher/benedikt-kessler
Contact person: Benedict Kessler
An essential element of collaborations and transfer of knowledge is the short-term visits of GENPRO members to Mentor Labs. During the reporting period eleven short-term visits to Mentor Labs have been realised.
The participants were engaged in:
1. Project planning, discussions about the Organisation of facilities, presentations of previous and current projects in Fleming labs and discussions about future joint grant applications.
2. Training in genomics and proteomics applications, performing experiments to set up collaborative projects, developing new computational tools for HTP genomics applications.
The objectives of this work package have been successfully executed. There was an extensive transfer of knowledge from MLs, which helped to acquire the know-how running the highly specialised and complex sequencing instrument and the mass spectrometer. As a result of the efficient knowledge transfer, the two facilities very quickly established the various sequencing and protein analysis technologies described above in WP2. In fact, within of about a year of operation the facilities were in position to offer high quality services in several different applications.
Mentor Lab 1 (Jiannis Ragoussis at Oxford University, UK) stopped functioning as Mentor Lab after the first year and joined BSRC Al. Fleming as member of GENPRO. At the same time Dr Ragoussis took charge of Fleming's Genomics facility. As described in Deliverable D3-2 two collaborations with Mentor Labs on future EU projects have been initiated.
Workpackage 4: Organisation of Workshops and Dissemination activities
This Workpackage had 4 objectives: Organisation of workshops, construction of web site, Organisation of seminar series at Fleming and presentations of GENPRO activities in conferences.
Workshop 1, "Workshop on Functional and Structural Proteomics" was organised with about 5 months delay on month 23 of the program.
Workshop 2, "Next generation sequencing methods and applications" were organised as planned in month 24 of the program.
They were advertised in GENPRO web site, in BSRC Al. Fleming web site, the web sites of major Greek universities and research centers, the web sites of two EU-ITN programs (DISCHROM and INTEGER) and through e-mailing to about 400 Greek and European biology labs.
As described in Deliverables 4-1 and 4-2 both workshops consisted a seminar / presentation part and a practical hands-on course in the facilities of BSRC Al. Fleming. The presentation part of the Proteomics workshop was co-organised with PROFI (Regpot program in IMBB-FORTH, Crete) and Dischrom (Marie Curie ITN program at Fleming). Both workshops attracted large audience: 89 and 120 people for Workshop 1 and Workshop 2, respectively. For the practical courses 12 and 20 students were selected. Some of the related activities included studies with animals. All of the activities of the program were in compliance with the ethical standards and requirements of the ethical review accompanying the contract.
Potential Impact:
GENPRO web site was constructed in the first month of the project. The web site can be accessed at: http://www.fleming.gr/en/investigators/Talianidis/genpro_overview.html
It contains the main information about the project including overview of the activities, personnel data, Mentor lab data, description of facilities, vacancies, workshop schedules and programs and scientific publications. The web site has been regularly updated by the coordinator. An important dissemination activity is the GENPRO initiative to organize publicly open seminar series at BSRC Fleming premises, by inviting external speakers from different biological fields. The thematic program had a common feature: emphasis on global analysis using modern genomics and proteomics approaches. The following invited seminars were organised:
2010-22-4 Ancient animal miRNAs and the evolution of tissue identity Dr Fay Christodoulou EMBL, Germany.
2010-27-5 Transgenerational Epigenetic Inheritance in Colliding Genomes and Dividing Cells Antonis Giakountis, Ph.D RNA silencing and Epigenetics, University of Cambridge, England.
2010-31-5 Cytokine signaling in inflammatory bowel diseases Prof. Markus Neurath Universit Asklinikum Erlangen.
2010-2-7 A discussion on Epigenetics Professor Emeritus Constantine Moiras University of Medicine of Athens.
2010-10-9 Lgr5 adult stem cells in tissue renewal and disease Nick Barker, Ph.D. Hubrecht Laboratory, Netherlands Institute of Developmental Biology.
2010-14-10 Transcription factor networks & long range interactions Professor Frank Grosveld Erasmus Medical Center, Rotterdam, The Netherlands.
2010-20-12 Drosophila models of human infections & carcinogenesis Dr Georgios Apidianakis Department of Surgery & Molecular Biology Harvard Medical School.
2011-28-01 Maping RNA-protein interactions in translation Dr. Yiota Kafasla Department of Biochemistry, Un. of Cambridge, UK.
2011-18-03 Regulation of immune responses by IKK-induced NF-kB1 p105 proteolysis Dr Steve Ley MRC-NIMR, London, UK.
2011-10-05 The Integrated Stress Response in Tumorigenesis: Problems and Opportunities for Therapeutic Intervention Costas Koumenis, Associate Professor Department Radiation Oncology, University of Pennsylvania, School of Medicine.
2011-11-05 RANKL and Osteoimmunology, Prof Hiroshi Takayanagi, Cell Signalling Department, Tokyo Medical and Dental University
2011-14-07 Id3 restricts the generation of thymic innate-like T lymphocytes, Dr Mihalis Verykokakis, Dept of Pathology & Committee on Immunology, University of Chicago.
2011-13-09 Leukaemia Stem Cells in Acute Myeloid Leukaemia, Dr Paresh Vyas, MRC Molecular Haematology Unit Weatherall Institute for Molecular Medicine Oxford, UK.
2011-10-10 Induced glioma-initiating cell models reveal new therapeutic targets, Dr Toru Kondo, Dept of Stem Cell Biology, Ehime University Proteo-Medicine Research Center, Japan.
2011-01-11 Macrophage inflammation and chemotaxis in mouse models of atherosclerosis, Dr Pieter Goossens, Cardiovascular Research Institute of Maastricht.
2012-19-04 Epigenetic control of the mobile genome: implications for cell identity and disease, Dr Valerio Orlando, Dulbecco Telethon Institute, IRCCS Fondazione Santa Lucia, Rome - Italy.
2012-19-10 Regulation of macrophage polarization By Akt kinases and miRNAs, Dr Christos Tsatsanis, Dpt. of Clinical Chemistry, School of Medicine, University of Crete. The above seminars attracted audiences between 80-120 people, represented about equally by scientists from BSRC Fleming and scientists from other institutions of Greece, mainly from Athens.
Another important dissemination activity is the construction, curation and open access availability of web resources for computational models in systems biology. This is based on computational tools developed by GENPRO members. The DIANA (Dna Intelligent analysis) site can be accessed at: http://diana.cslab.ece.ntua.gr/
In addition, work performed using GENPRO facilities have been highlighted in audio podcast interview by M. Fousteri:
Biobytes, February 7, 2011 Journal of Cell Biology, The Rockefeller University Press. Online, audio podcast on the regulation of Nucleotide Excision DNA Repair (Overmeer et al., 2011).
GENPRO members have also published 28 scientific papers in which the facilities were used. These publications are listed in Deliverable D2 and also in the web site of GENPRO:
http://www.fleming.gr/en/investigators/Talianidis/genpro_publications.html
Below is a selection of representative publications:
Koliaraki V, Roulis M, Kollias G. 2012, "Tpl2 regulates intestinal myofibroblast HGF release to suppress colitis-associated tumorigenesis.", J Clin Invest. 122:4231-42.
Nikolaou K., Tsagaratou A., Eftychi C., Kollias G., Mosialos G., Talianidis I . 2012, "Inactivation of the deubiquitinase CYLD in hepatocytes causes apoptosis, inflammation, fibrosis and cancer.", Cancer Cell, 21: , 738-750.
Reczko M, Maragkakis M, Alexiou P, Papadopoulos GL, Hatzigeorgiou AG. 2012, "Accurate microRNA Target Prediction Using Detailed Binding Site Accessibility and Machine Learning on Proteomics Data.", Front Genet. 2011;2:103. 2011;2:103.
Yiakouvaki A, Dimitriou M, Karakasiliotis I, Eftychi C, Theocharis S, Kontoyiannis DL 2012, "Myeloid cell expression of the RNA-binding protein HuR protects mice from pathologic inflammation and colorectal carcinogenesis.", J Clin Invest. 122(1):48-61.
Gkiafi Z, Panayotou G. 2011, "Comparative Proteomic Analysis Implicates COMMD Proteins as Epstein-Barr Virus Targets in the BL41 Burkitt's Lymphoma Cell Line.", J Proteome Res. , 10:2959-68.
Schmidt D, Wilson MD, Ballester B, Schwalie PC, Brown GD, Marshall A, Kutter C, Watt S, Martinez-Jimenez CP, Mackay S, Talianidis I, Flicek P, Odom DT. 2010, "Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding." Science. 328(5981):1036-40.
Results from the Genomics services of GENPRO also contributed the filing of one patent application:
TNF superfamily trimerization inhibitors, Inventors: Georgios Kollias, Eleni Douni
Application Number: P95195PC00. Priority Date: 12 August 2011.
A very important activity of GENPRO members during the reporting period is the participation in scientific study groups disseminating new knowledge gained by emerging high throughput genomics and proteomics technologies. Dr George Kollias is the Coordinator of the Study Group on Animal Models (SGAM) funded by the European League Against Arthritis (EULAR). The aim of EULAR SGAM was to draft a guidance document to provide recommendations on current bottlenecks and limitations in predictive animal modelling and to guide future directions that will enhance innovation in arthritis pre-clinical research. The Study Group met at the EULAR House in Zurich, Switzerland, on March 18th and 19th 2010 and the guidance document was published on April 24, 2011 in the Annals of Rheumatic Diseases. See link: http://www.ncbi.nlm.nih.gov/pubmed/21628308.
The use of emerging technologies in -omics profiling (including chromatin structure, epigenetic, miRNA, transcriptional, post-transcriptional and proteomic analysis), to facilitate the alignment of mouse models to human disease, is a key point in the document, which concludes that "the association of phenotypes to molecular profiles (gene, protein and metabolite expression) offers an invaluable tool for unveiling pathogenic mechanisms, pathways and targets and also for discovering predictive biomarkers for diagnosis and treatment."
Finally, GENPRO members presented their related work in several international conferences. Major presentations during the reporting period were as follows:
Iannis Talianidis, Epigenetic mechanisms regulating liver development, metabolism and disease, XXIV International Complement Workshop. Chania, Oct 10-15. 2012. ~300 participants.
Iannis Talianidis, Epigenetic mechanisms regulating liver development, metabolism and disease, Epigenetics Conference Budapest, Hungary Sept 20-22. 2012 ~150 participants.
Kostas Nikolaou, Panagiotis Moulos, George Chalepakis, Hisanobu Oda, Danny Reinberg and Iannis Talianidis, PR-Set7-mediated H4K20 methylation controls genome integrity and metabolic pathways in liver. 10th EMBL Conference in Transcription and Chromatin Heidelberg Aug. 25-28. 2012 ~300 participants.
Samiotaki, M. "Analysis of protein-protein interactions: quantitave proteomic strategies". 2nd Greek Orbitrap User Meeting. Crete, Greece. 23-24 April 2012. ~40 participants.
Vlachonasios K, Poulios S, Topouzis S, Samiotaki M and Panayotou G, Synergistic action of histone acetyltransferase GCN5 and CLAVATA1 receptor kinase negatively affect ethylene responses. 23rd International Conference on Arabidopsis Research, Vienna, Austria, July 3-7, 2012. ~200 participants.
Oehrl W., Cotsiki M., Samiotaki M. and Panayotou G. Regulatory role of the M3/6 dual-specificity phosphatase in JNK signalling. 37th FEBS & 22nd IUBMB Congress, Sevilla 4-9 September 2012. ~150 section participants.
Samiotaki, M. Recent advances in pharmacoproteomics. 1st Conference of Pharmaceutical Sciences, Athens, Greece. 27-30 April 2012. ~100 participants.
Aidinis V. Autotaxin and LPA signalling in the pathogenesis of chronic inflammatory diseases 2011 FASEB Summer Research Conference Lysophospholipid mediators in health and disease. August 14-19, Lucca, Italy. (2011). ~120 participants.
V.S. Gartaganis, M. Samiotaki, G. Panayotou, S.P. Gartaganis. Proteomic analysis of aqueous humour from patients with Pseudoexfoliation syndrome. SOE Congress, Geneva, 5-7 June 2011. ~200 participants.
Ioannis Pandis, Caroline Ospelt, Niki Karagianni Maria Denis, Martin Reczko,Carme Camps, Artemis Hatzigeorgiou, Jiannis Ragoussis, Steffen Gay and George Kollias. Association of microRNA-221/222 and -323-3p with rheumatoid arthritis via predictions using the human TNF transgenic mouse model. 8th Global Arthritis Research Network (GARN) Meeting, November 14-16, 2011. ~200 participants.
Maria Fousteri. Genome wide approaches in DNA repair. ICGC Meeting in Epigenetics and non-coding RNAs. Amsterdam Nov 6-10. 2011. ~100 participants.
Iannis Talianidis. Operation of a transcription factor network driving liver development. 9th International Conference on Pathways, Networks, and Systems Medicine. Aegean Conferences Chania, June 10-15. 2011 ~200 participants.
Ikonomou G., Kostourou V., Landegren U., Soderberg O., Samiotaki M., Panayotou G. Interplay between oncogenic K-ras and wild type H-ras in colorectal cancer. EMBO Conference Series "SPATIAL 2011", 15-19 May 2011, Engelberg, Switzerland, ~ 100 participants.
V. Aidinis. Autotaxin and Phospholipid signalling in Chronic Inflammation. - Advances in Immunology and Cancer Biology workshop. 15-17 April 2011, Bogazici University, Istanbul, Turkey. ~ 150 participants.
Fousteri M. Deciphering the role of transcription and chromatin remodelling in DNA repair. Conference on Responses to DNA damage: from molecular mechanisms to human disease. Egmond aan Zee, The Netherlands, April 3-8, 2011. Approx. 350-400 participants.
Ikonomou G., Samiotaki M., Kostourou V., Pintzas A., Panayotou G. Interplay between oncogenic K-ras and wild type H-ras in Caco2 cell transformation. 61st Meeting of Hellenic Society of Biochemistry & Molecular Biology, 15-17 October 2010, Alexandroupoli, Greece. 400 participants.
Nikolaou K. and Talianidis I. CYLD inactivation in liver. 61st Meeting of Hellenic Society of Biochemistry & Molecular Biology, 15-17 October 2010, Alexandroupoli, Greece. 400 participants.
M. Karagiannopoulos, M. Samiotaki, G. Panayotou, ME. Lekka. Effect of propanil and diazinon on the protein profile of Tetrahymena. - 1st International Proteomics Conference on Crete-IPCC01. Crete, Greece. 7 and 8 October 2010. ~100 participants.
M. Samiotaki, M. Panopoulou, G. Panayotou, A. Ikonomidis. RNase-mediated post-transcriptional regulation of gene ompA seems to be the major mechanism of carbapenem heteroresistance in A. baumannii. ECCMID-2011. 21st European Congress of Clinical Microbiology and Infectious Diseases. Milan, Italy 7-10 May 2011. ~250 participants.
Samiotaki M and Panayotou G. 1st Greek Orbitrap User Meeting. Crete,Greece. 9th October 2010. ~30 participants.
G. Kollias. The pros and cons of interfering with TNF-dependent functions. The Second Kitasato Symposium: New Prospects for Cytokines, Palais am Festungsgraben, Berlin, Germany May 27-29, 2010 ~ 150 participants.
G. Kollias. Tumour necrosis factor and inflammatory disease. Mouse models for human diseases. The Royal Society London, UK, May 19-21 2010 ~ 150 participants.
I. Talianidis. Lysine methylation regulates E2F1-induced cell death. 9th EMBL Conference on Transcription and Chromatin. Heidelberg August 28-31. 2010 ~300 participants.
Iannis Talianidis. Transcription Regulation in Liver. FASEB Summer Research Conference, Liver Growth, Injury and Metabolism: Basic and Applied Biology, Snowmass Village, Colorado August 15-20, 2010 ~ 300 participants.
Workpackage 5: Evaluation and Management
The objectives of Workpackage 5 (Evaluation and Management) are:
a. Setting up the Management and Advisory Committee.
b. Monitoring the implementation of the program and reporting achievements.
c. Evaluation of the success of the program.
The Management Committee was set up at the start of the project. It is composed of the GENPRO Researchers (Aidinis V., Fousteri M., Hatzigeorgiou A., Kollias G., Kontoyannis D., Panayotou G., Strouboulis J.). During its first unofficial meeting in November 2009, it specified the composition of the Advisory Committee, which was approved in the first official Management and Advisory Committee meeting in December 2. 2009 at BSRC Fleming. The Advisory Committee is composed of the heads of the Mentor Labs (Jiannis Ragoussis, Benedikt Kessler, Axel Imhof and Nikolaus Rajewsky).
The Management Committee has met 5 more times during the duration of the project:
In April 22. 2010, in October 12. 2010, in March 11. 2011, in January 10. 2012 and in November 12. 2012. All meetings were at the premises of BSRC Al. Fleming.
In the first Management Committee meeting held together with the Advisory Committee, discussions and decisions were made on the following issues:
1. Hiring new personnel.
2. Specifications of desired DNA sequencer and Mass Spectrometer.
3. Timetables and Deliverables of the project.
In the subsequent Management Committee meetings discussions and decisions were made on:
1. Administrative matters related to tenders and job contracts.
2. Room assignments and Organisation of facilities.
3. Scientific projects using the equipment in the new facilities.
4. Organisation of workshops.
5. Web sites and Organisations.
6. Seminar series at Fleming.
In the last Management Committee meeting (Nov. 2012) was also attended by ML2 and ML3. In this meeting the achievements of the project were evaluated and plans for the possibilities of future expansion, upgrades were discussed.
Summary of the major decisions made on interim Management Meetings:
1. Selection of 3 scientists hired by GENPRO in the first round (Dec. 1 2009).
2. Purchase of ABI-SOLID4 DNA sequencing platform.
3. Purchase of Orbitrap-XL mass-spectrometer.
4. Approval of GENPRO Web-site content.
5. Assignment of new rooms for the instruments, expansion of the areas of the existing facilities.
6. Approval of 4 short-term visits to Mentor labs.
7. Approval of invited speakers for Fleming Seminars.
8. Tentative plans for Workshop 1 and Workshop 2.
9. Decision of postponing Workshop 1 to October 6. 2011.
10. Operation plan for the facilities to allow the use by external scientist.
11. Selection of 2 scientists hired by GENPRO in the second round of announcement (Sept. and Dec. 1 2010).
12. Final Workshop programs and sending invitations.
13. Approvals of additional visits to MLs and participation in conferences.
14. Decision of replacing Dr Mouratos with Dr Dimopoulos for the last period of the program.
15. Decision of extending Service Contracts for the instruments by one year payable from other sources.
16. Approval of the list of services provided by the two units to external users.
In the last meeting (November 2012) the Management Committee reviewed the status and the progress of the project and provided the overall assessment shown below:
Overall Assessment
After the first assessment in March 2011, significant progress has been made. Combined with the first period's conclusions, the GENPRO project significantly contributed to enhancing the research potential of BSRC Al. Fleming:
a. The project provided new state of the art instrumentations for the Genomics and Proteomics facility of BSRC Al. Fleming. The facilities are equipped with the most modern instrumentation. This allows performing frontier research at the institute.
b. The project contributed to the improvement of BSRC Research potential by making it possible to hire highly qualified Experienced Researchers and repatriate an established Greek scientist.
c. The project aided the development of new contacts with scientists working in leading centers of Europe.
The overall progress of the project was high. All of the deliverables have been achieved. The main points concerning the progress of the project are:
Goals achieved:
a. Purchased and installed ABI SOLID4 High-throughput Sequencer.
b. Purchased and installed Thermo Scientific Orbitrap XL Mass Spectrometer.
c. Hiring of high quality personnel with expertise specified in the contract has been completed.
d. Repatriation of hER has been achieved.
e. Training of personnel has been completed.
f. Instruments test runs have been performed and first tests with experimental samples have been run. Data were collected and quality controls have been evaluated.
g. Instruments have run several experimental samples.
h. Several experimental approaches have been set-up and used routinely.
i. The facilities reached the level to provide services for outside users in several sequencing and proteomics applications.
j. Twinning collaborations with Mentor labs have been initiated.
k. Web site has been constructed and several other means of dissemination (other web tools, webinar, scientific publications, conference presentations and participation in study groups) have been successfully realised.
Deviations from the original plan:
a. Significant delay in the purchase of the instruments (DNA sequencer and Mass-spectrometer).
b. Postponement of Workshop-1 by 5 months.
Despite the above delays Workshop-1 was organised with success. The delay of instrument purchase eventually did not affect the implementation of the goals. The success of the program was also evident by the number of new competitive grant applications from GENPRO members that were successful for funding. New grants in which the proposed topics require the existence of an in house Genomics or Proteomics facility are:
5 Greek grants (Aristeia and Synergasia program)
3 Greek grants (ESPA Post-doctoral program)
1 Greek grant (Thales program)
1 ERC Advanced Investigator Award
1 ERC Consolidator Award.
GENPRO members have also submitted 5 independent applications for the Marie Curie ITN and HEALTH program, which are currently being evaluated. Furthermore the new genomics facility represents the basis of a novel initiative that aims at networking Greek genomics labs. Funding for this has been obtained from the Greek General Secretary of Science and Technology (grant number: 09SYN-13-901). Another very important development in BSRC Al. Fleming where the GENPRO facilities played pivotal role is the Center's participation in the ESFRI Infrastructure project, the European Infrastructure for phenotyping and archiving of model mammalian genomes. Greece, through the General Secretariat for Investments and Development, has recently committed 3,9 million Euros for the development of the Greek node of Infrafrontier, which is coordinated by BSRC Al. Fleming. Both the Genomics and Proteomics facilities will continue to support INFRAFRONTIER-GR, whose activities are described in http://www.fleming.gr/infrafrontier-GR/
Project website: http://www.fleming.gr/en/investigators/Talianidis/genpro_overview.html
Iannis Talianidis
BIOMEDICAL SCIENCES RESEARCH CENTER ALEXANDER FLEMING
34, Alexander Fleming Street, 16672 Vari, Athens, Greece.
Phone. +30 210 965 3773
Fax +30 210 9653934
e-mail talianidis@fleming.gr