European Biomarkers Summit and Proteomics Europe 4-5 September 2007 Amsterdam, The Netherlands

Distinguished Faculty Ruedi Aebersold Huub Hoefsloot Peter Schulz-Knappe Professor, ETH Zurich Associate Professor, University of Director, Proteome Sciences Amsterdam Hans Aerts Salvatore Sechi Professor, Academic Medical Centre, Markus Kalkum Director, National Institute of Diabetes and University of Amsterdam Beckman Research Institute Digestive and Kidney Diseases

Anders Alderborn Stig Linder Michael Smith Associate Professor, Uppsala University Professor, Karolinska Institute R&D Scientist, Invitrogen Corporation

Karl-Friedrich Becker Theo Luider Serhiy Souchelnytskyi Group Leader, Technical University of Professor, Centre for Biomics, Erasmus Associate Professor, Head of Laboratory, Munich, Institute of Pathology University of Rotterdam Karolinska University Hospital Ruedi Aebersold Robert Beynon John McCafferty Jan Tavernier Head, Proteomics and Functional Senior Project Leader/Principal Group Leader, Medical Protein Research, Genomics Group, Investigator, Sanger University of Gent Institute Dolores Cahill John Timms Professor of Translational Science, Michael Pierce Group Leader, University College London University College Dublin Professor, University of Georgia Mathias Uhlén Geert De Jaeger Matej Orešič Professor, KTH Biotechnology Professor, VIB Dept. Plant Systems Senior Research Scientist, VTT Technical Biology, Ghent University Research Centre Richard Watts Dolores Cahill Marketing Manager Pharma/Biotech, Elisabetta Fortunati Richard Pembrey QIAGEN Senior Scientist, University Medical Centre Functional Proteomics Segment Manager, Utrecht Sigma Aldrich Christer Wingren

Complete Speaker List Complete Speaker Assistant Professor, Department of William Gallagher Steve Pennington Immunotechnology, Lund University, Associate Professor, University College Professor of Proteomics, Conway Institute Sweden Dublin for Biomolecular and Biomedical Research, University College Dublin Marketa Zvelebil Radoslav Goldman Group Leader: Bioinformatics & Systems Assistant Professor, Georgetown University Roland Pieters Biology, Ludwig Institute for Cancer Roy Goodacre Associate Professor, Utrecht University Research, Royal Free and University Roy Goodacre College School of Medicine Professor of Biological Chemistry, Robert Possee Group Leader, CEH Oxford Heinz Zwierzina Professor, Innsbruck University of Medicine Jascha-Nikolai Rybak Research Scientist, ETH Zurich

Salvatore Sechi Profiling Kinases and Phospho-Sites with Antibody- Protein Arrays for Biomarker Discovery and Protein Based Methods for Disease Biomarker and Drug Expression Profiling Target Discovery

Course Tutor: Dr. Steven Pelech, Professor, University of Course Tutor: Dr. Christer Wingren, Assistant Professor, British Columbia, Canada Lund University, Sweden.

Learning Objectives Include: Learning Objectives Include: • Learn about the nature of the kineome, • Master the basic concepts underlying protein phosphatome and phosphoproteome in humans and microarrays other species • Learn how to design protein arrays for, in particular, Mathias Uhlen • Be aware of the serious limitations of genomic biomarker discovery and protein expression profiling analyses for cell signalling studies analysis • Become familiar with a range of proteomics • Become familiar with the data analysis and methodologies available to track cell signalling bioinformatic tools Corporate Sponsors proteins, including their advantages and limitations • Learn about recent development in protein arrays Training Courses Training • Find out about the real performance of commercial applied to biomarker discovery and protein expression antibodies and antibody microarrays for biomarker profiling discovery Registration Option ‘Pelech’ Registration Option ‘Wingren’

Both courses will be held on 3 September, the Wingren course in the morning, the Pelech course in the afternoon. Further details online.

All brochure details are correct at time of print. Please see web sites for updates.

Sponsorship and exhibition opportunities Contact Paul Raggett SELECT [email protected] BIOSCIENCES +44 (0)1787 315117 Delivering the Difference European Biomarkers Summit Day One

Biomarkers Clinical Applications Enabling Tools for Biomarkers Identification

Biomarkers in Early Clinical Drug Development A Human Protein Atlas for Normal and Cancer Tissues Heinz Zwierzina, Professor, Innsbruck University of Medicine Mathias Uhlén, Professor, KTH Biotechnology Proteomics has proven to be a potential tool to discriminate The Human Protein Atlas portal (www.proteinatlas.org) between benign and malignant tumour lesions. How the contains 1.2 million high-resolution images corresponding to technique also holds promise for monitoring functional effects more than 1500 antibodies towards human proteins. The use of investigational agents and is expected to provide us with of the database as a tool for medical research, in particular new biomarkers for evaluation of response and/or resistance, for biomarker analysis in various patient cohorts, will be will be described. discussed.

Understanding Biological Systems Using Validation of Novel Breast Cancer Biomarkers Arising and Proteomics from Re-Analysis of Publicly Available Datasets via Roy Goodacre, Professor of Biological Chemistry, University Tissue Microarrays and Automated Quantitative of Manchester Scoring Models for Immunohistochemistry An overview of metabolomics and inductive reasoning for William Gallagher, Associate Professor, University College turning metabolite data into knowledge will be presented, Dublin spatial metabolic fingerprinting and proteomics will also be A new strategy to mine data from transcriptomic screens discussed. and subsequent validation of candidate biomarkers on tissue microarrays will be presented. Digital slide scanning Coffee Break and Networking in Exhibition Hall approaches were employed to facilitate both manual and automated scoring. Metabolomics Strategy to Identify Tissue Specific Drug Effects Critical Success Factors in the Development and Matej Orešič, Senior Research Scientist, VTT Technical Implementation of Biomarkers in Drug Development Research Centre Richard Watts, Marketing Manager Pharma/Biotech, QIAGEN Metabolomics will be demonstrated to provide an excellent Novel technologies useful in biomarker discovery and approach to characterise phenotypes and lead to discoveries development, as well as a case study of the technology of new biomarkers of complex physiological conditions. It can implementation capabilities in pharma partnerships, will be complement and augment genomics and proteomics which described. requires a powerful data integration platform to combine different types of information. Coffee Break and Networking in Exhibition Hall

Signal-Amplifying Biomarkers for the Diagnosis of New Molecular Tools for Ultra-Sensitive Analysis of Invasive Fungal Infections Biomarkers Markus Kalkum, Beckman Research Institute Anders Alderborn, Associate Professor, Uppsala University A novel proteomic methodology that discovers and exploits Proximity ligation will be presented as a new technology which fungal protease activities as signal amplifying biomarkers for permits highly specific analysis of protein biomarkers. The the diagnosis, prognosis and monitoring of invasive fungal technology, which is now applied for biomarker evaluation, infections, will be presented. can specifically detect very low amounts of biomolecules in blood and even single copies in situ. Lunch in Exhibition Hall followed by Poster Viewing Chemical Proteomics for the Identification of Vascular Markers of Disease Jascha Rybak, Research Scientist, Group of Professor Dario Neri, ETH Zurich The use of vascular biotinylation procedures, followed by a mass-spectrometry-based comparative proteomic analysis of biotinylated proteins to identify novel markers of pathology, which are easily accessible from the bloodstream and ideally Why not extend your stay in suited as targets for antibody-based drug delivery applications Amsterdam? Simply quote ‘Select will be presented. Biosciences’ when you book your room to obtain the negotiated Statistical Validation of Biomarkers rate for the length of your stay. Huub Hoefsloot, Associate Professor, University of Amsterdam Visit BiomarkersSummit.com or In –omics data the number of possible markers is much ProteomicsEurope.com for further larger then the number of experiments. This type of data information. structure can easily lead to chance results in biomarker discovery. Strategies to find statistically valid biomarkers will be presented.

Drinks Reception Proteomics Europe Day One

Quantitative Proteomics Coffee Break and Networking in Exhibition Hall

Quantitative Proteomics and Systems Biology Protein Expression Ruedi Aebersold, Professor, ETH Zurich Attempts to comprehensively analyse the proteome of eukaryotic cells, the challenges such projects face and outline strategies to overcome them will be discussed. Proteomic Scale Generation and Validation of Recombinant Antibodies Coffee Break and Networking in Exhibition Hall John McCafferty, Senior Project Leader/Principal Investigator, Wellcome Trust Sanger Institute Biological Reference Materials for Discovery and A consistent source of monoclonal antibodies to the wealth of Validation of Biomarkers in Tissues and Body Fluids newly discovered genes in the genome would be of huge value Peter Schulz-Knappe, Director, Proteome Sciences to the research community. The feasibility of this by selecting Lack of precision and reproducibility hamper proteomics and characterising 7000 unique recombinant antibodies to analysis. It will be described that spiking of biological 300 antigens, will be demonstrated. reference materials labelled with Tandem Mass Tags™ allows for relative quantification of the entire sample proteome with High Throughput Generation of Baculovirus highly improved precision and CV. Expression Vectors for Protein Expression Robert Possee, Group Leader, CEH Oxford Strategies for Proteome Simplification and An automated high throughput system for the generation Quantification of recombinant baculoviruses has been produced to permit Robert Beynon, Head, Proteomics and Functional Genomics parallel construction of expression vectors in insect cells, Group, University of Liverpool without the need for plaque purification. The process involved It will be demonstrated that proteomics requires novel thinking is essentially a one-step transfection. and novel strategies to become quantitative and global. Building the Cell Cycle Interactome by Protein Lunch in Exhibition Hall followed by Poster Viewing Complex Purifications from Plant Cell Suspension Cultures Geert De Jaeger, Professor, VIB Dept. Plant Systems Biology, Ghent University Post-Translational Modifications: Glycomics A high throughput TAP based technology platform was raised to isolate protein complexes from plant cell suspension cultures, which will be presented. It is currently applied to gradually build a cell cycle interactome for Glycans and Peptides for Detection of Hepatocellular Arabidopsis thaliana. Proof of concept for complex isolation Carcinoma will be shown for a set of cell cycle related proteins. Radoslav Goldman, Assistant Professor, Georgetown University Drinks Reception Analyses of peptides and glycans represent newly tested strategies for discovery of cancer biomarkers. The application of these methods to the detection of hepatocellular carcinoma identified a set of candidate biomarkers that classify HCC with greater than 90 % prediction accuracy. Call for Posters Chemical Probes for the Detection of Carbohydrate Binding Proteins Roland Pieters, Associate Professor, Utrecht University Presenting a poster at this event is a perfect Using protein-carbohydrate interactions to determine opportunity to share your research and knowledge, important biological processes, many of which are linked to whilst bring many opportunities to network with disease, will be discussed. Chemical probes were prepared to colleagues. enable the detection, ultimately for diagnostic purposes, of Deadline: 8 July 2007 certain carbohydrate binding proteins from protein mixtures. ePosters.net will be presenting an Tools for Glycomics: Relative Quantitation of Glycans award and certificate for the best by Isotopic Permethylation Using 13C Methyl Iodide poster presented at this event. Michael Pierce, Professor, University of Georgia The most complex post-translational modification of proteins, A submission form and further details can be found online. glycosylation, is influencing and regulating diverse physiologic processes. Analysis of glycan structures is an important component of the emerging field of glycoproteomics and the use of mass spectrometry has enabled the investigation of the glycan repertoire of organisms. European Biomarkers Summit Day Two

Biomarkers Profiling and Discovery Disease Specific Biomarkers

Discovery of Cancer and Autoimmune Biomarkers A Search for a Biomarker for Monitoring and Utilizing Serum Antibody Profiling on Protein Predicting Diabetes Microarrays Salvatore Sechi, Director, National Institute of Diabetes and Michael Smith, R&D Scientist, Invitrogen Corporation Digestive and Kidney Diseases Protein microarrays have been successfully applied to The use of new proteomic biomarker for the development investigate the circulating antibody profile in several disease of an assay for detecting pre-diabetes and diabetes will states. Invitrogen has developed a high content human protein be discussed. Several projects mainly involving protein microarray containing over 8,000 full-length, functional characterization by mass spectrometry and proteomic proteins for the discovery of novel and known autoantibody profiling of plasma samples will also be explained. markers associated with cancer and autoimmune disease. A Serum Efficiacy Biomarker for Clinical Trials: High-Throughput Disease Proteomics Using Measuring Tumour Cell Apoptosis and Necrosis in Recombinant Antibody Microarrays Serum During Cancer Therapy Christer Wingren, Assistant Professor, Department of Stig Linder, Professor, Karolinska Institute Immunotechnology, Lund University, Sweden Our presentation will discuss the release of different molecular We will discuss a new state-of-the-art recombinant antibody forms of cytokeratin-18 (caspase-cleaved and total CK18) microarray technology platform for high-throughput (disease) from dying tumour cells which can be used to measure tumour proteomics of non-fractionated proteomes that has been cell death modes in vitro and in vivo. Data suggests that CK18 devised. Based on a non-invasive blood test, the platform serum biomarkers may be useful for early prediction of the can be used to detect potentially diseased-associated serum response to anthracyclin-based therapy in breast cancer. protein biomarker signatures, providing novel opportunities for biomarker screening and disease diagnostics. Coffee Break and Poster Award Ceremony

Coffee Break and Networking in Exhibition Hall Proteomic Characterization of Tumoural Markers Correlated with Erbb2/Her2 Over-Expression and Screening and Profiling Protein Expression in Human Metastasis in Breast Cancer Cancer Plasma Using Antibody Array Technologies John Timms, Group Leader, University College London Richard Pembrey, Functional Proteomics Segment Manager, The receptor tyrosine kinase ErbB2 (HER2/Neu) will be Sigma Aldrich discussed. This is a marker of breast cancer whose over Antibody arrays will be presented as a powerful tool for rapid expression has been detected in ~30% of cases and is expression profiling of proteins and that may potentially be correlated with poor prognosis and an increased likelihood of applied to biomarker discovery in diseased serum samples. metastasis.

The Quantitative Nature of Fourier Transform Mass Close of Conference Spectrometry in Biomarker Discovery Theo Luider, Professor, Centre for Biomics, Erasmus University of Rotterdam The use of Maldi Fourier transform ion cyclotron resonance mass spectrometry (MALDI FTMS ) in gel free, label free approaches to quantify large numbers of natural occurring and tryptic generated peptides in cerebrospinal fluids and laser microdissected tissues will be discussed.

Lunch in Exhibition Hall followed by Poster Viewing

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Proteomics Technologies Disease Proteomics

Interaction Screening on Protein Microarrays Quantitative LC-MS Serum Analysis for Gaucher Dolores Cahill, Professor of Translational Science, University Disease College Dublin Hans Aerts, Professor, Academic Medical Centre, University Technology improvements towards measuring interactions on of Amsterdam protein microarrays will be presented. A label-free LC-MS method, including novel analysis concepts, will be described for absolute and relative quantification pSTIING is a New Publicly Accessible Web-Based of Gaucher disease related biomarkers and indicators in Application and Knowledgebase serum. The LC-MS activity levels will be shown to be in good Marketa Zvelebil, Group Leader, Bioinformatics & Systems agreement with biochemical assay levels. Biology, Ludwig Institute for Cancer Research, Royal Free and University College School of Medicine Protein Extraction from Formalin-Fixed Clinical pSTIING will be presented as a new publicly accessible web- Tissues for Nanoscale Biomarker Analysis based application and knowledgebase of molecular associations. Karl-Friedrich Becker, Group Leader, Technical University of It also supports the direct cross-correlation of experimental Munich - Institute of Pathology results with interaction information in the knowledgebase, which A novel technology for isolation of intact, soluble and currently analyses and clusters gene expression, proteomic and immunoreactive proteins from formalin-fixed tissues has phenotypic datasets. been developed. Applications of this method for measuring abundances of protein markers and profiling of deregulated The MAPPIT Toolbox: Strategies to Analyse Molecular signalling pathways in various diseases will be presented. Interactions in Intact Cells Jan Tavernier, Professor, VIB Department, Medical Protein Lunch in Exhibition Hall followed by Poster Viewing Research, Ghent University MAPPIT (Mammalian Protein-Protein Interaction Trap) is a Proteomics Analysis of Alveolar Macrophages in cytokine receptor-based two-hybrid method that operates Sarcoidosis Patients Suggests an Increased Apoptosis in intact mammalian cells. Applications of MAPPIT in HIV Rate and a Dysregulation of Iron Metabolism research will be discussed. Elisabetta Fortunati, Senior Scientist, University Medical Centre Utrecht Coffee Break and Networking in Exhibition Hall Proteomic technology is a powerful tool for identifying novel prognostic, diagnostic and therapeutic markers. Its application in the study of Sarcoidosis yields novel information about the pathophysiology of this incurable lung disease will be discussed.

Coffee Break and Poster Award Ceremony

Venue Biomarker Discovery and Validation in Biomedicine/ Clinical Proteomics Steve Pennington, Professor of Proteomics, Conway Institute Our venue for this for Biomolecular and Biomedical Research, University event is the Hilton College Dublin Amsterdam, which After a brief introduction to biomarkers, from discovery to is in one of the City’s clinical utility, the application of different proteomics strategies most exclusive in recent and on-going biomarker discovery projects in pancreatic and prostate cancer and predictive toxicology will areas, close to be presented. Amsterdam’s best shopping streets Towards a Database of Breast Cancer Proteomics: and the City’s commercial and financial Centre. Proteome Profiling of Human Breast Cancer The Hotel borders a canal and overlooks its Showed Unique Pattern of Protein Expression and Phosphorylation own garden and marina. Serhiy Souchelnytskyi, Associate Professor, Head of Laboratory, Karolinska University Hospital Special rates for accommodation are available Proteomics has been proven to improve cancer diagnostics to event attendees, please see either and treatment. Research for cancer-related changes in the BiomarkersSummit.com or human breast epithelial cells proteome will be detailed. Found proteins analysed by systems biology tools can be used as ProteomicsEurope.com for details. markers and drug targets.

Close of Conference European Biomarkers Summit and

Proteomics Europe - Registration Form Exhibitors

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