Proteomics is the new "omics" on the block. This conference is designed to showcase protein-protein interactions, protein array production, protein profiling, and the resulting potential of protein research for drug discovery. Rarely acknowledged, economics is an important aspect of the "omics" family as well. Although proteomics does remain hypothesis-driven, advances in technologies such as chips, arrays, and informatics mean this burgeoning enterprise has the potential application to turn "omics" from red into green. CHI's Proteins to Profits is designed to provide information in a precise, productive manner. Plan to attend Proteomics-Europe and Protein and Peptide Arrays to view the entire picture of the new "omics."

Corporate Sponsor

Sponsoring Organization

Sponsoring Publications

BioArray News The Journal of Peptide Research PharmaGenomics Proteomics ProteoMonitor

Web Partners

Lab-on-a-Chip.com Pharmacogenomicsonline.com

Scientific Advisors
Dr. Dolores Cahill, Max-Planck-Institute of Molecular Genetics
Dr. Joerg Hoheisel, Deutsches Krebsforschungszentrum
Dr. Michael Taussig, The Babraham Institute

Speakers
Dr. Mark Allen, Advion Biosciences Ltd.
Dr. Kevin A. Auton, NextGen Sciences Ltd.
Dr. Jonathan M. Blackburn, Sense Proteomic Limited
Dr. Pascal Bolon, WITA Proteomics AG
Dr. Dolores Cahill, Max-Planck-Institute of Molecular Genetics
Dr. Robert Cavallo, PerkinElmer Life Sciences
Dr. Joerg Hoheisel, Deutsches Krebsforschungzentrum
Dr. Ian Humphery-Smith, University of Utrecht and Glaucus Proteomics B.V.
Dr. Mats Inganäs, Gyros AB
Dr. Amelie Karlström, Royal Institute of Technology (KTH)/Stockholm Center for Physics, Astronomy and Biotechnology (SCFAB)
Dr. Victor Morozov, Russian Academy of Sciences
Dr. Steffen Nock, Zyomyx, Inc.
Dr. Stefan R. Schmidt, GPC-Biotech AG
Dr. Barry Schweitzer, Molecular Staging Inc.
Dr. Michael Taussig, The Babraham Institute
Dr. Markus F. Templin, University of Tübingen
Dr. Andreas Wiesner, Ciphergen Biosystems Ltd.

Keynote Address
Human Protein Arrays and Their Applications

Production
PISA Method
Electrospray-Fabricated Protein Microarrays
Rolling Circle Amplification
CD Microlaboratory
COVET™ Process

Present Prospects
Functional Analyses
Protein Microarray-Based Assays
Cytokine Quantification
ProteinChip® Technology
Resolving the Problems

Promise
High-Density Protein Arrays
Multiplexed Expression Profiling
Signal Transduction Profiling
Toxicity Marker Identification
Affibody™ Ligands

 

Monday, March 25

17.15-17.45 Early Registration
Registrants of Proteomics-Europe are welcome to attend the Tuesday afternoon session 
of Protein and Peptide Arrays at no extra cost.

 

Tuesday, March 26

13.00-14.00 Conference Registration

 

Production

14.00 Chair's Opening Remarks
Dr. Michael Taussig, Chairman, European Science Foundation Programme in Functional Genomics, and Head, Technical Research Group, The Babraham Institute

14.05 Protein Identification and Characterisation using Automated Chip Based Nanoelectrospray Mass Spectrometry
Dr. Mark Allen, Vice President of European Operations, Advion BioSciences Ltd.
Mass spectrometry (MS) is a valuable analytical tool for protein characterisation. Matrix assisted laser desorption ionisation (MALDI) and electrospray ionisation (ESI) provide complementary molecular information on proteins and protein digests. To-date, MALDI has the advantage of automation while ESI is more easily coupled with nanoscale separations. This lecture will describe the ESI ChipTM, an automated chip based nanoelectrospray platform and its application to protein identification and characterisation.

14.35 Protein Arrays from DNA by Cell-Free Expression (PISA Method)
Dr. Michael Taussig
In the PISA (protein in situ array) method, tagged functional proteins are made by cell-free expression directly from PCR DNA and simultaneously immobilized at a surface. This enables a protein array to be made in a single step from DNA, avoiding cloning, cell-based expression, and protein purification. We believe it will have advantages for proteins or individual domains where cloned genes are not available or where the proteins cannot be functionally expressed in cell-based expression systems. We will describe the combination of PISA and ribosome display technology to analyze protein-protein interactions in a library-against-library format.

15.05 Electrospray-Fabricated Protein Microarrays in Diagnostics, Screening, and Proteome Research
Dr. Victor Morozov, Senior Scientist, Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences
The electrospray deposition technique in combination with different immobilization procedures is used to fabricate two types of protein microarrays. In the first microarray proteins are cross-linked in glutaraldehyde vapor and show a good efficiency in screening interactions with small metabolites (MW < 1 kD) labeled with radioactive isotopes and in "fishing in the whole metabolite pool with protein microarray as a bait" procedure using ESI/MS for identification of the bound metabolites. Covalent immobilization of proteins via dextran spacers is used in the second type of multi-antigen (allergen) microarrays designed for immunodiagnostics. Microarrays of proteins with unknown function can be used to rapidly find their partners among all the metabolites, proteins, DNA, and polysaccharides in a living cell and, thus, to help in assigning their function.

15.35 Poster and Exhibit Viewing, Refreshment Break

16.15 Simultaneous Quantification of Multiple Proteins in a CD Microlaboratory Array
Dr. Mats Inganäs, Senior Scientist, Diagnostic Applications, Gyros AB
A CD microlaboratory platform has been developed for quantification of multiple proteins in crude samples. A sandwich type of fluorescent assay has been implemented for multiple parallel analyses in CD utilizing discrete affinity capturing beds with different binding specificities corresponding to the analytes of interest. Aliquots of sample are processed in parallel by controlling flow rate over the affinity bed using centrifugal force. Bound proteins are further detected by sequential addition of complementary fluorescent ligand followed by in situ detection of fluorescence. Sub-nanomolar concentrations of serum proteins in 100-nl sample volumes have been accurately quantified in less than 15 minutes.

16.45 Functional Protein Arrays in Drug Discovery
Dr. Jonathan M. Blackburn, Chief Scientific Officer, Sense Proteomic Limited
We have developed sequence-independent approaches that involve modifying each individual gene at the cDNA library level in a single pot such that, following clonal separation and expression of the library in an appropriate host, each recombinant protein has an affinity tag appended at either the C or N terminus. We will show data on the output of our COVET™ process and will show that the tag can then be used to impart a commonality to downstream purification and immobilization of the proteins in an automation-compatible format. Clearly, the value of our method relies on proteins retaining their function once they have been oriented and tethered to a surface, irrespective of whether the format is microwell plate- or chip-based. We have performed a range of assays to demonstrate the viability and function of N and C terminally tagged proteins tethered to different substrates. Examples include (i) enzymatic activity of glutathione S transferase, luciferase, alanine racemase, horseradish peroxidase, and b-galactosidase; (ii) DNA-binding activity of the transcription factors NF-kB, NFAT, and p53; (iii) on-chip phosphorylation of P53 mutants; (iv) binding of small molecules; and (v) protein-protein interactions.

17.15 Panel Discussion

17.45 Networking Reception co-sponsored by Cambridge Healthtech Institute and the Bavairan State Ministry of Economics, Transport, and Technology

19.00 Close of Day

 

Wednesday, March 27

8.00 Poster and Exhibit Viewing and Light Continental Breakfast

 

Present Prospects

8.30 Chair's Remarks
Dr. Joerg Hoheisel, Functional Genome Analysis, Deutsches Krebsforschungzentrum

8.35 Use of Complex Peptide- and Antibody-Microarrays in Functional Analyses
Dr. Joerg Hoheisel
The Division of Functional Genome Analysis at the DKFZ is involved in the development of technologies for the analysis of DNA-encoded function and its regulation. Current work emphasizes DNA-, protein-, and peptide-microarrays. Apart from addressing chemical and biophysical issues, such as highly parallel in situ peptide synthesis and optimization of surfaces of protein arrays, for example, the resulting methods are immediately put to the test in relevant, biologically driven projects.

9.05 Protein Microarray Technology
Dr. Markus F. Templin, Microarray Technology, NMI-Natural and Medical Sciences Institute, University of Tübingen
Biochip technology allows the simultaneous analysis of thousands of molecular parameters within a single experiment. Most of the current applications focus on DNA array technology for gene expression analysis or the detection of single nucleotide polymorphism. However, any kind of ligand binding assay that uses an immobilized capture molecule for the detection of the binding of analyte from a solution can be miniaturized. For example, sandwich antibody assays can be miniaturized and parallelized to be performed in a microarray format. Autoantigen microarrays can be used to screen in parallel for the presence of autoantibodies from minimal amounts of patient sera. Immobilized antigens can be used to determine in-parallel selectivity and affinity of antibodies. Data of protein microarray-based assays that are currently performed at the NMI will be presented and discussed.

9.35 Array-Based High-Throughput Screening and Quantification of Cytokines
Dr. Robert Cavallo, Product Manager- Protein Microarrays, PerkinElmer Life Sciences
We describe two types of antibody miniarray systems suitable for high-throughput screening and quantification of proteins. The use of exceedingly small quantities of capture antibody immobilized in microspots facilitates ambient analyte assay conditions. Under these assay conditions, the fractional occupancy of capture antibody is independent of sample volume. Analyte concentrations are thus measured with greater sensitivity and potentially greater speed. The high-density cytokine chip is suitable for rapid high-throughput simultaneous screening of multiple cytokines in conditioned media, patient's sera, and cell lysate. The low-density cytokine chip is used for further quantitative analysis of cytokine expressions.

10.05 Poster and Exhibit Viewing, Refreshment Break

10.45 ProteinChip® Technology for Rapid Protein Profiling, Biomarker Discovery, and Validation
Dr. Andreas Wiesner, Field Scientist, Germany, Ciphergen Biosystems Ltd.
The ProteinChip® System enables rapid profiling and biomarker discovery from crude biological samples on a single integrated platform. The system consists of three components: ProteinChip Arrays that allow direct application of biological samples like serum or urine, a time-of-flight mass spectrometer, and specially developed software for the comparative analysis and further evaluation of the generated data. Arrays are available with different types of chromatographic surfaces (e.g., reverse phase, cationic/anionic exchange). On each type of surface a specific subpopulation of proteins from the sample is retained, according to its biophysical properties. Consequently, low-concentration potential biomarkers are often enriched and can be easily detected for the very first time. Highly hydrophobic proteins and proteins with extreme isoelectric points that are often excluded from 2D gels can be analyzed with this technology. Furthermore, the range below 20 kDa, normally neglected by traditional methods, is easily accessible. The software allows comfortable handling of the data and offers a number of features specially developed for the comparative analysis of large numbers of spectra. Software components are incorporated that rapidly and effectively speed up the discovery and validation process for potential diagnostic markers or new therapeutic targets without the need to develop antibody arrays.

11.15 Protein Biochips: Resolving the Problems of This Emerging Technology
Dr. Kevin A. Auton, Chief Executive Officer, NextGen Sciences Ltd.
As with all emerging technologies that show great potential, the difficulties of reducing "exciting theory" to "real-life practice" is an unyielding problem for most research scientists. Since as early as 1991, researchers have found the major difficulties associated with the use of protein biochips to be (1) attachment of the protein to a solid surface such that it retains functionality, (2) achieving appropriate high levels of sensitivity for the assay, (3) developing a universal method to attach Protein Recognition Molecules (typically, but not limited to, antibodies, Ab fragments, or phage) to the surface of the biochip, and (4) achieving reproducibility. During this presentation, NextGen's solutions to these issues will be presented and illustrated with experimental data from studies that include protein expression analysis of complex samples from breast cancer samples, recombinant protein expression monitoring in cell culture, and antibody screening.

11.45 Panel Discussion

12.15 Lunch (on your own)

 

Promise

13.00 Chair's Remarks
Dr. Dolores Cahill, Group Leader, Protein Technologies, Max-Planck-Institute of Molecular Genetics

13.35 High-Density Protein Arrays: Generation and Applications
Dr. Dolores Cahill
The array format has revolutionized biomedical experimentation and diagnostics, enabling ordered high-throughput analysis. During the past few years, classic solid phase substrates such as microtitre plates, membrane filters and microscopic slides, were turned into high-density, chip-like structures. Here the generation of a non-redundant, human Unigene-Uniprotein set will be described. This set contains over 10 000 different (non-redundant) human proteins derived from a human fetal brain cDNA expression library. These proteins have been arrayed on membranes and on glass slides (protein chips). The results of screening these high density, high content protein arrays with antibodies and serum from patients with auto-immune disease, will be presented. Applications of high density protein in proteomics will also be described.

14.05 Protein Microarrays: New Tools to Unravel the Complexity of the Proteome
Dr. Steffen Nock, Senior Director of Biochemistry, Zyomyx, Inc.
This talk will describe the development and application of high-density protein microarrays. Major emphasis will be on multiplexed expression profiling studies of serum and cytoplasmic proteins using antibody microarrays as well as on protein-protein interaction chips in combination with mass spectrometry to analyze protein complexes. In the outlook, novel label-independent detection technologies for high-density arrays will be discussed.

14.35 Functional Protein Microarrays for Signal Transduction Profiling
Dr. Stefan R. Schmidt, Group Leader, Protein Biochemistry/Proteomics, GPC-Biotech AG
The DNA microarray revolution has largely contributed to the identification of novel differentially regulated targets. However, in most cases a functional analysis of those targets still remains unsolved. Ideally, the required analytical approach is also conducted in a highly parallel mode on protein microarrays. We have focused on profiling the activity of kinases. This is of particular interest because these are primary drug targets frequently involved in malignant cellular developments. In the context of drug discovery, protein arrays are valuable tools to solve complex problems. By combining our HT protein expression and purification technology with our integrated protein array-based characterization that also includes automated image analysis, we were able to analyze a broad set of different molecules involved in signaling processes. Substrate arrays can be utilized for analyzing the qualitative and quantitative specificities of kinases and the effect of activators or inhibitors. We will show a series of examples on array-based activity profiling including the process of how to generate and analyze those arrays.

15.05 Poster and Exhibit Viewing, Refreshment Break

15.45 Toxicity Marker Identification for the Development of Diagnostic Arrays
Dr. Pascal Bolon, Director of Marketing, WITA Proteomics AG
High-throughput protein chip tools could provide an important means of evaluating the toxicity profiles of lead compounds in human cell lines prior to costly clinical evaluation. The process of chip design and implementation is highly involved, requiring the identification of toxicity-related proteins from cells of interest, the anchoring of selected toxicity marker antibodies to a chip-based platform, and optimization of reaction conditions for the detection of toxicity-related proteins from cellular samples. Here we address the first aspect in the design of a chip-based drug evaluation tool, the identification of hepatotoxicity markers against a number of toxic drug classes using high-resolution NEPHGE proteomics. The ability to correctly assess protein abundance changes and identify proteins exhibiting toxicity-related changes is critically associated with separation resolving power. Case studies utilizing WITA's technology in determining proteome changes in cell lines will be presented.

16.15 Using Affibody™ Ligands in Protein Chips for Proteomics
Dr. Amelie Karlström, Royal Institute of Technology (KTH)/Stockholm Center for Physics, Astronomy and Biotechnology (SCFAB)
Affibody AB, a proteomics and biotherapy company, uses cutting-edge protein engineering technologies to create novel small, robust protein ligands that mimic antibodies in a variety of biological and functional applications. Affibodies™ can be engineered to have desired specificity and affinity, while also being highly robust to withstand a broad range of physical conditions, including pH and elevated temperature. The specific binding properties that can be engineered into each Affibody™ allow it to have very high specificity and the desired affinity for a corresponding target protein. Affibodies™ will enable novel therapeutic strategies and will enable drug discovery by offering speed, accuracy, high throughput and robustness in proteomic research.

16.45 Panel Discussion

17.15 Close of Conference

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Hotel Information
Arabella Sheraton Grand Hotel
Arabellastraße 6
Munich D-81925, Germany
T: 49-89-9264-0 • F: 49-89-9264-8699

Room Reservations:
T: 49-89-9264-8521 • F:49-89-9264-8509
Room Rates:
163.00 Euro/single • 178.00 Euro/double
Cut-off Date: March 1, 2002

Please call the hotel directly to make your room reservation. Identify yourself as a Cambridge Healthtech Institute conference attendee to receive the reduced room rate. Reservations made after the cut-off date or after the group room block has been filled (whichever comes first) will be accepted on a space-and-rate-availability basis. Rooms are limited, so please book early.

Call for Posters
Cambridge Healthtech Institute encourages attendees to gain further exposure by presenting their work in the poster sessions. Please fill out the registration form, with the poster title and primary author. To ensure inclusion in the conference binder, a one-page summary must be submitted and registration must be paid in full by February 15, 2002.  Click here for poster instructions

Call for Sponsorship and Exhibit Opportunities
CHI’s protein meetings are regarded internationally as pivotal for those most involved with this exploding area of biotech. Proteomics-Europe and Protein and Peptide Arrays are designed to complement both the technology and application of proteomics. We strongly encourage any company with services or products related to bioinformatics, protein informatics, genomic databases, protein-protein databases, data management, structure and identification algorithms, annotation techniques, protein structure, target validation, X-ray crystallography, and lab automation, as well as microarrays for protein printing, binding, detection, and other applications, to consider sponsoring or exhibiting at this event. Sponsorship is the ideal avenue to prominently elevate your company’s presence and influence in this focused market. There are various sponsorship levels available and the higher ones include an exhibit space. The exhibition hall will run from March 25-27, 2002 and cover both conferences. For more information on sponsorship opportunities or to reserve a booth, please contact Deborah Brooks at 781-972-5412 or dbrooks@healthtech.com.

Exhibitors and Sponsors as of 3/19/02
Advion BioSciences, Inc.
Agilent Technologies Deutschland GmbH
Bavarian Ministry for Economics Affairs
Nonlinear Dynamics Ltd.
PerkinElmer Life Sciences
Rentschler Biotechnologie GmbH & Co.
Sidec Technologies AB
Structural Bioinformatics, Inc.
ThermoFinnigan

Immediately following  PROTEOMICS-EUROPE, March 25-26, 2002, Arabella Sheraton, Munich, Germany

 

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