3 rd Central and Eastern European Proteomic Conference
6-9 October 2009
Budapest, Hungary

Organisers:

Draft Report

Summary

The Central and Eastern European Proteomic Conference (CEEPC) is organised annually with the aim of exchanging information and new results between people interested in proteomics in the region. It is a great opportunity for young people to present their results on an international level and to gain experience. This year annual meetings of the Hungarian, Austrian and Czech proteomic societies were organised under the auspices of CEEPC. Support from ESF enabled students from Europe to participate at the meeting.

The conference was a great success, which is confirmed by the high number of participants (151) from over 10 countries including 33 students.. The main goal was to widen each others knowledge about different aspects of proteomics: fundamentals; biological, biochemical and clinical applications; post-translational modifications and analytical methodologies also to present and discuss recent results and to promote collaboration among various laboratories.

The programme consisted of oral sessions, two poster sessions and a conference dinner. All together there were twelve oral sessions, for every session there was a prominent scientist from the particular area in order to summarise the state of the art in the field. During the three days we could hear several interesting lectures from the most emerging fields of proteomics.

The first day was dedicated to clinical proteomics (e.g. high performance proteomics) and to novel strategies for proteomics (e.g. pathway search engine, methodology developments for high throughput analysis of prokaryotic proteomes). Also in the afternoon during the coffee break parallel with the poster session there was a workshop discussing the interaction between genetics and proteomics.

The second day lectures in clinical proteomics (e.g. brain proteomics, proteome analysis of human tears) continued along with new topics like stem cell proteomics, quantitation in proteomics and advanced mass spectrometric approach for the analysis of peptides on planar separation media.

On the third day lectures were presented in topics such as spatially-resolved proteomics, imaging of biomarkers, analysis of animal proteome and membrane proteomics.

During the conference there were two poster sessions, both in the afternoon. People could walk around and inform themselves about the posters they found interesting. There was an award for the best poster both days chosen by a scientific committee.

The conference dinner which took place on a boat cruising on the river Danube seemed to be a very good choice according to the feedback of the participants.

Scientific Content

The Central and Eastern European Proteomic Conference is organised annually with the aim of exchanging information and new results between people interested in proteomics in the region. It is a great opportunity for young people to present their results on an international level and to gain experience. This year the 3rd Central and Eastern European Proteomic Conference was organised in Budapest. The main organiser was the mass spectrometry and proteomics department of the Chemical Research Centre. The meeting was held at Hotel Benczur, which provided enough space and a secluded atmosphere at a reasonable price.

Proteomics, like other “omics”, depends heavily on advanced analytical technology. Instrumentation is very expensive and needs substantial resources from individual countries. This is one of the prime reasons why the proteomics technology in former Central and Eastern European countries lags behind the US or Western Europe. Communication among laboratories in this region is sporadic, which hinders development and coordination and which is also a stumbling block towards successful project applications. With these in mind, Austrian, Czech, German, Hungarian, Italian, Slovak, Swiss and Russian scientists came together and launched the Central and Eastern European Proteomic Conference series; the first meeting was held in Prague (2007), the second one in Jena (2008).

The aim of this regional conference is to disseminate information, help form stronger bonds and to promote collaboration among various laboratories. All important aspects of proteomics were covered – fundamentals; biological, biochemical and clinical applications; post-translational modifications and analytical methodologies. Medium-size conferences, like CEEPC, rotating among various countries may stimulate and deepen research and collaboration.

Plenary lecturers (http://www.chemres.hu/ms/3rdceepc/Scientific_program.html), ensured a high level of scientific content. The low costs helped students in participating at the meeting and seeing the ‘state of the art' at first hand. Also support from ESF enabled researchers and students from Eastern Europe to attend the meeting.

The meeting programme consisted of oral sessions, two poster sessions, and a conference dinner. A workshop was also held discussing the interaction between genetics and proteomics during the CEEPC conference. For every oral session, 1 or 2 prominent scientists from the particular area have been invited to summarise the state of the art in a particular field. Four or five 15-minute lectures were selected from submitted abstracts. Sessions have been organised by scientists from participating countries.

The first day was dedicated to clinical proteomics and to novel strategies for proteomics. The topic of the first plenary lecture was high performance proteomics and biomarker discovery. The difficulties in the analysis of all proteins in a complex protein mixture were discussed. In these cases a huge amount of data is produced from a single sample and the following analysis and validation becomes the time limiting step. On the other hand proteomics raises high expectations in finding new and reliable biomarker for human diseases. In the lecture they applied micro dissection combined with saturation DIGE technology and mass spectrometry and succeeded in finding new biomarker candidates for liver cirrhosis caused by HCV infection. This technology allowed the quantitative proteome analysis of a few thousand cells from individual patient samples and to get reproducible proteomics data pointing to new biomarker candidate proteins for liver cirrhosis. This method demonstrated that high performance proteomics is the basic principle for reliable results which allowed the authors to discover new biomarker candidates for liver cirrhosis using minute amounts of patients' material.

In the next plenary lecture (Harald Michak, Germany) the basic principles and clinical diagnostic applications of proteome analysis using capillary electrophoresis coupled to mass spectrometry were summarized. CE-TOF-MS technology, together with software solutions to evaluate the vast amount of data, enables reproducible analysis of 1000 – 6000 peptides and proteins in a sample within 45-60 min and is applicable for biomarkers discovery and routine clinical procedures. The advantages of CE were emphasized such as robustness, reproducibility and resolution, along with reduced costs, run-time, and sensitivity towards interfering compounds. These features make CE an ideal separation technology. The author focused on the non-invasive detection of renal diseases, cancer, arteriosclerosis, monitoring of transplants and response to therapy. The data indicate that an “ideal single biomarker”, allowing definition of disease with high accuracy, does not exist. However, a panel of biomarkers with good discriminatory features can be combined to a specific model.

The strength of the human urine proteome database of thousands of comparable data is the ability to define and validate biomarkers based on samples from patients with similar diseases, enabling identification of truly disease-specific biomarkers.

In the topic of novel strategies for proteomics the first lecture was about pathway search engine. The aim of most MS-studies concerning signaling pathways is to obtain new information on the signaling mechanism. After study completion and publication, this information ends up in databases, e.g. KEGG Pathway Database, TRANSPATH etc. Unfortunately the information in these databases, however valuable, cannot be relied upon for quantitative prediction of signaling pathways. The author (Roman Zubarev, Sweden), demonstrated, first in the proof-of-principle study, and then in the application to a real-life system that unbiased conversion of quantitative expression proteomics data into semi-quantitative status of activated signaling pathways and key nodes is possible. He reported on progress in designing a Pathway Search Engine (PSE) for expression proteomics and its first applications to tissue samples. Their challenge was to design a sensitive, specific and robust procedure that identifies activated signaling pathways, determining for each pathway the degree of activation, its uncertainty and the p-value. Results were shown where data obtained in collaborative research are used for the development of the quantitative and statistical aspects of pathway analysis.

Another lecture (Jon Amster, USA) in this topic described the development of new tools for proteomic analysis that are based on accurate mass measurement. They pursued accurate mass measurement as a method for protein identification as it offers higher throughput and lower computational effort. The presentation described improvements to the specificity of peptide identification that have been achieved by application of mass defect labeling and isotope labeling as well as by developments in accurate mass measurement by Fourier transform mass spectrometry.

Also in the afternoon partly parallel with the poster session there was a workshop discussing the interaction between genetics and proteomics. There were 2 presentations during the Workshop and a lively discussion afterwards.

The second day lectures in clinical proteomics (e.g. brain proteomics, proteome analysis of human tears) continued along with new topics like stem cell proteomics, quantitation in proteomics and advanced mass spectrometric approach for the analysis of peptides on planar separation media.

The lecture about targeted neural stem cell differentiation and related cell based therapy in spinal cord injury was very exciting. They anticipated that characterisation of protein changes related to stem cell differentiation can help define suitable biomarkers that might be necessary for partially differentiated cells to optimally progress to a fully differentiated stage of neurons and glial cells after grafting. Furthermore, understanding of repair after spinal cord injury at the protein level enables the identification of candidate targets for future cell based transplantation therapy and facilitates the functional recovery after spinal trauma.

There was a plenary lecture about cholesterol homeostasis and how disruption of this process may lead to disease. To investigate the expression of enzymes involved in cholesterol metabolism a proteomics approach was applied. The first step of cholesterol metabolism in brain occurs in neurons. To investigate the effects of cholesterol and its fellow sterols on cholesterol homeostasis neurons and a neuronal cell line have been treated with 24S-hydroxycholesterol, a cholesterol metabolite, and 24S,25-epoxycholesterol, a sterol synthesised in parallel to cholesterol by the same enzymes. The effects on the proteome have been monitored by both iTRAQ and SILAC methodologies. Both sterols have the effect of inhibiting the expression of enzymes of the cholesterol biosynthetic pathway.

Lecture on proteome analysis of human tears discussed that analysis of tear proteins may be of diagnostic value. Their aim was to examine the tear fluid proteome from non-invasively collected human tear samples as well as to compare the protein profile in tears of healthy persons and patients with diabetic retinopathy. ProteinPilot and Mascot softwares were used for protein identification with this technique they were able to identify 43 proteins, 13 of them have not been identified previously in tears using proteomic techniques. Among the proteins identified by ProteinPilot in various samples, 15 were useful for quantitative comparison. The ratios of proteins in the different stages of the disease were compared to the protein content of healthy donors and were indicative to the disease state.

On the third day lectures were presented in topics such as spatially-resolved proteomics, imaging of biomarkers, analysis of animal proteome and membrane proteomics.

The investigation of membrane proteins is still subject to strong limitations. Two obvious problems are the limited solubility of membrane proteins preventing the use of standard 2D-PAGE approaches as well the limited accessibility of typical transmembrane helices to trypsin digestion. Alternative experimental approaches to address these problems were discussed. First the double SDS technique enabling one to focus also extremely hydrophobic membrane proteins, and 2 nd the use of less specific enzymes, like elastase and pepsin.

Venoms from a variety of animals, not only snakes, were already successfully applied as pharmaceuticals to control unbalanced cardiovascular functions, blood clotting dysfunctions, to treat Parkinson's or Alzheimer's disease or have been shown to inhibit tumors. Some proteins isolated from vipers' venoms belong to the CAP (cysteine-rich secretory proteins, antigen 5 and pathogenesis-related 1 proteins) protein superfamily, which links them structurally to certain allergens of plant foods and pollen. They studied the relationships of allergens to other members of protein superfamilies to learn more about the evolution of allergenicity. The discovery of relevant new pharmaceutical lead structures and drug targets are thought to benefit from snake venom peptidomics as well as proteomics.

The last plenary lecture discussed a new protocol combining different imaging technologies for the analysis of various tissue types. This multimodal approach was demonstrated in a study of a variety of diseases such as breast cancer and arthrosclerosis. The rapid development of new mass spectrometric imaging technology provides the MS community with new tools to examine detailed biomolecular distributions on surfaces. This opens the door for true molecular histology in biomedicine.

For more details of the 3rd Central and Eastern European Proteomics Conference visit the conference website.

Assessment of the results & impact of the event on the future direction of the field

The CEEPC conference series has a strategic impact on science in two respects. First, it covers an important, fast growing field (proteomics) and second, it act as a catalyst in Central and Eastern Europe, an emerging area of the European Community.

Proteomics covers a wide, interdisciplinary and intersectorial field. Proteomics has direct interrelation with genetics: Partly because changes in gene expression are reflected in the protein composition; and partly because proteins do influence gene expression. In systems biology; which tries to understand and describe biological behaviour, proteins and genes fill in different mosaics to make an overall pattern. Proteomics is closely connected to analytical chemistry; biochemistry, biology; and have direct relevance to the biomedical field. All these disciplines were covered at the CEEPC meeting, as shown in the titles of the following selected lectures: „High Performance Proteomics - a successful way to Biomarkers”, „Proteome Analysis Using Capillary Electrophoresis Coupled Mass Spectrometry: Basic Principles and Clinical Diagnostic Applications”, „A proteomic approach to analysis of synaptosomes from mouse models of Alzheimer's disease”. Proteomics is also intersectorial: At the 3rd CEEPC meeting, similarly to the previous ones, participants came from different sectors, mostly from universities and research institutes, but a fair number also from the industry (both large multinationals and SME) and from hospitals.

CEEPC, as the name suggests, also fills an important role establishing and furthering contacts and collaborations in Central and Eastern Europe. In this fast growing area (both with respect to geografic area and field of science) it is especially important to support international collaborations. This is an improtant key to successfull future European projects and networks. The student travel grant from ESF was especially useful to help training a new generation of young scientists. 

Undoubtedly, it was a great success and evidenced by the attendance and the quality of presentations. The next meeting is awaited eagerly with great anticipation and will be held at the Vienna University of Vienna in Vienna, Austria from the 29th August to the 2nd September 2010.

Programme