4th ESF Workshop on Affinity Proteomics
23-25 March 2009
Alpbach, Austria

Organisers:

Draft Report

Summary

The ESF ProteomeBinders workshop, held March 23-25 2009 in Alpbach (Austria) was attended by 99 academic and industrial participants from Europe and the US. The meeting reviewed the current state of production of binding molecules, by both conventional and recombinant methods, the applications of binders in proteomics and the bioinformatics requirements. In addition to 18 main speakers there were 23 poster presentations. The meeting was co-funded by the ESF programme on Frontiers of Functional Genomics and the EC FP6 ProteomeBinders coordination action. The programme consisted of two days of talks, with time set aside for outdoor activities and continuing discussion during the early afternoon, a layout which proved very popular with all participants.

Scientific Content

The aim of the meeting was to address the widely acknowledged and increasingly urgent need for comprehensive resources of well characterised affinity binding reagents for the detection of human proteins in health and disease. Characterisation of the human proteome is a major post-genome challenge with huge significance in both basic and medical research, as well as for the biotechnology and pharmaceutical industries. It calls for systematic generation of binders against all genome-encoded proteins and their variant forms (splice variants, modifications, etc). The most familiar of such molecular reagents are antibodies, yet despite the commercial availability of a large number of antibodies, currently only a fraction of the proteome is covered. Moreover, the unreliable quality of commercially available antibodies is a frequently encountered concern. At the same time, recombinant engineered protein scaffolds are becoming viable alternatives. Since its inception, ProteomeBinders has actively planned a route for high throughput production of binders of all types against human proteins, including evaluation of available resources, standardised production and quality control protocols, binder-based application tools and a bioinformatics infrastructure.

In the opening session Michael Neuberger (Cambridge) described recent work on the mechanism of hypermutation of antibodies – one of the key aspects of antibody production in vivo. The novel format of single domain antibodies was discussed by Serge Muyldermans (Brussels) with respect to camel antibodies and Frank Grosveld (Rotterdam) who described their production in transgenic mice. The use of such recombinant domains for live cell imaging was described by Tony Kossiakoff (Chicago).

The design and applications of novel non-antibody binder molecules were discussed by Andreas Pl?ckthun (Zurich) who has based binder structures on ankyrin and armadillo repeat proteins. In relation to proteomics applications of binders, Larry Gold (Boulder) described the use of DNA aptamers against more than 800 human proteins. Three speakers discussed the role of peptides and peptide binding reagents: peptide antibodies to enrich biomarkers from plasma were described by Terry Pearson (Victoria, Canada); Frank Breitling (Heidelberg) described peptide microchips with up to 40,000 peptides on a single array; Shohei Koide (Chicago) described their novel affinity clamping approach which is specialised to particular classes of peptides.

On the second day Mathias Uhlén (Stockholm) introduced the newly released database portal Antibodypedia developed to allow sharing of data on validation of antibodies. Sandra Orchard (EBI, Hinxton) defined a new system of reporting guidelines using minimal information principles (MIAPAR, minimum information about a protein affinity reagent). The work in John McCafferty 's lab (Cambridge) in generating phage display antibodies on a global scale was linked to a proteome atlas in the mouse. Brian Kay (Chicago) described applications in zebrafish. The parallel project to ProteomeBinders in the USA, at the National Cancer Institute was presented by Tara Hiltke (Bethesda). Production of binders by refolding in E. coli was described by Itai Benhar (Tel Aviv) which can lead to considerable cost reductions.

Novel applications in proximity assays for protein protein interactions was described by Ola Soderberg. The final talk by Carl Borrebaeck (Lund) summarised the meeting and the work carried out in his group on biomarker detection in different cancers.

The posters covered a wide range of techniques from antigen and epitope selection to array based expression analysis on proteomic chips.

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

The ESF ProteomeBinders workshop on Affinity Proteomics brought together a critical mass of leading European and US academic and industrial players in affinity proteomics, contributing to global networking in the field. Feedback suggested that this was one of the best meetings in the field. The meeting significantly contributed to progress in affinity proteomics by linking novel developments in binder production with applications in proteome analysis where the long term aim is to establish a full set of reagents for analysis of the human proteome. Essential to this ambition of are systematic and comprehensive collections of specific affinity reagents directed against all human proteins, including splice variants and modifications. While the most familiar affinity reagents are antibodies and their fragments, the meeting also promoted awareness of engineered forms of protein scaffolds and nucleic acid aptamers with similar diversity and binding properties which are becoming viable alternatives. The meeting also encouraged the linkage between current initiatives in Europe and the USA, where partners of the ProteomeBinders consortium was able to interact with the Clinical Proteomics Initiative underway at the National Cancer Institute at Bethesda. A further impact of the meeting was in relation to funding by the EC Framework 7 programme. Several of the attendees were co-applicants of a proposal to the EC health call and were able to focus the ideas for their application through discussions in Alpbach. The application ProtAffin was subsequently approved with funding of 11M€.

Programme
Monday 23.3.2009 – Arrival and Registration

14:00 – 17:00 Registration open at the Conference Centre Alpbach

19:30 Get together at Hotel Alpbacherhof

20:00 Workshop Opening Dinner at Hotel Alpbacherhof

Tuesday 24. 3. 2009 – First day of Workshop

8:00 – 10:00 Registration open at the Conference Centre

Morning Session Chair: Mike Taussig

8:30 Mike Taussig: Welcome

8:45 Michael Neuberger: Evolving antibodies

9:15 Serge Muyldermans: Pros and cons of being a camel

9:45 Frank Grosveld: Evolving human antibodies in the mouse

10:15 Tony Kossiakoff: Receptor-mediated cytoplasmic delivery of synthetic antibodies for live cell imaging

10:45 Discussion

11:00 Poster session and coffee break

15:30 Poster session and coffee break

Après Ski Session Chair: Ulf Landegren

16:00 Andreas Plückthun: Novel binding proteins by design and evolution

16:30 Larry Gold: High density quantitative proteomics at ELISA-like limits of detection

17:00 Terry Pearson: Anti-peptide antibodies for proteomics applications

17:30 Frank Breitling: High-density peptide arrays

18:00 Shohei Koide: Affinity Clamps: Targeted affinity reagents for peptide motifs

18:20 Discussion

19:00 Departure for dinner at Roßmoos from Conference Centre

19:30 Dinner at Roßmoos

Wednesday, 25. 3. 2009 – Second day of Workshop

Morning Session Chair: David Sherman

8:45 Mathias Uhlén: Antibodypedia – a portal for sharing antibody and antigen validation data

9:15 John McCafferty: Ligand binders: from antigen to application

9:45 Brian Kay: The zebrafish protein and antibody core

10:15 Tara Hiltke: Raising the bar - NCI's antibody characterization pipeline

10:35 Sandra Orchard: MIAPAR - The minimum information about a protein affinity reagent

11:00 Poster session and coffee break

15:30 Poster session and coffee break

Après Ski Session Chair: Marius Ueffing

16:00 Itai Benhar: Inclonals - IgG and IgG-fusion proteins produced in E. coli by refolding

16:30 Marcus Hämmerle: Proteomic analysis separates Barrett's esophagus and esophageal adenocarcinoma from healthy controls by distinct T cell populations

17:00 Ola Söderberg: Detection of endogenous protein interactions in cell lines and tissue sections by in situ PLA

17:20 Carl Borrebaeck: Affinity proteomics in translational research

17:50 Final Discussion

19:00 Buffet Dinner and Party at Conference Centre