ESF/EU MolTools Workshop:
Ligand Binding Molecules against the Human Proteome

Clare College, Cambridge, UK
7-8 September, 2004

Organisers:

Mike Taussig: Babraham Institute, Cambridge
Andreas Plückthun: Zurich University, Zurich
John McCafferty: Sanger Centre, Hinxton, Cambridge

Background:

While sequencing and annotation of the human genome will identify all the genes in the DNA sequence, understanding the expression, distribution, and function of the encoded proteins is still in relative infancy. Partly this is a result of the sheer scale of the numbers of individual components; compared with the ~30,000 genes, the existence of alternative splicings and post-translational modifications (PTMs) means that there may be more than 10 times that number of individual protein species in the proteome, many of them functionally interconnected. It is fundamentally important to be able to detect, quantify and characterise all relevant proteins in tissues and fluids in health and disease. This effort requires a comprehensive collection of specific ligand-binding reagents against the members of the proteome including PTMs. The most familiar and frequently used of such binding molecules are antibodies, but there are also other possibilities based on novel molecular scaffolds or nucleic acids. They must be accompanied by the development of high throughput binder-based assay systems, and applications in diagnostics and therapeutics. The desirability of a comprehensive and standardised collection of binding molecules against the proteome has frequently been pointed out and this is therefore an excellent time to initiate a discussion of the issues involved.

Specific workshop aims:

The aim will not be simply to 'parade' different types of binders, but to explore whether a binder collection can be made on a genome wide scale. To draw an analogy with the human genome project, we are just at the stage of discussing the best strategies before thinking about how it would be organised.

The first issue is therefore how to carry out the project at the technical level and to define a pathway, concentrating particularly on key issues of availability of high quality cDNAs and pure protein, types of binders and selection methods.

Secondly, if it were agreed that the project is feasible in principle, how would it be organised in practice? Even if funds were available, it might not be easy to implement because of the 'factory' requirements (large scale, high throughput binder selection and production). Would there be one production centre or several, organised as a European consortium with several labs contributing, or 'top down' in one place?

Venue:

Clare College, Cambridge, UK
Participants will be accommodated in the College (optional).
Sessions will take place in the College.

Dates:

September 6-8, 2004

Registration:

Registration is now closed.

Programme:

Monday 6th September

18.00 Welcome drinks in Clare College Scholars' garden, Buffet in Small Hall

20.00 Session 1. Magnitude of the problem
What is it all about? Goals and scope of the workshop. Current status of the genome. How many proteins are there? Bioinformatics

- Mike Taussig, Andreas Plückthun, John McCafferty, Ulf Landegren: Introductions
- Ian Dunham (Sanger) Human genome and annotation
- Victor Jongeneel (Lausanne) Annotation, splice variants, bioinformatics

~21.30 End of day / visit pub?

Tuesday 7th September

09.00 Session 2. DNA collections/expression
Where will the target proteins come from? How complete are cDNA collections, how good are they? What are the best expression systems to use?

- Bernhard Korn (Heidelberg) cDNA collection, in vivo / in vitro expression
- Martin Yuille (Cambridge) cDNA collection
- Joshua LeBaer (Boston) FLEX consortium
- Mike Dyson (Sanger) Expression
- Christian Cambillau (Marseille) Expression

10.45 Coffee

11.15 Session 3. Binders and selection methods (1)
How to get the binders? What should they be? Antibodies, recombinant and nontraditional binders.

- Andreas Plückthun (Zurich) Overview of selection technologies
- Michael Feldhaus (Pacific Northwest Lab) Yeast display of antibodies
- Federico DeMasi (Heidelberg) High throughput selection of hybridomas
- Mathias Uhlen (Stockholm) Polyclonal antibodies

12.45 Lunch in Great Hall

14.15 Session 3. Binders and selection methods (2)
- John McCafferty (Sanger) Recombinant antibodies
- Mingyue He (Babraham) Ribosome display
- Andrew Bradbury (Los Alamos)
- Jim Marks (San Francisco)
- Serge Muyldermans (Brussels) Single domains

16.00 Tea

16.20 Session 3. Binders and selection methods (3)
- Andreas Plückthun (Zurich) Ankyrin scaffolds
- Per-Åke Nygren (Stockholm) Affibodies
- Larry Gold (Boston) RNA aptamers
- Jean Toulme (Marseille) Aptamers

~17.45 End of day

19.00 Drinks followed by dinner at Peterhouse

Wednesday 8th September

09.00 Session 4. Problems of cross-reactivity and sensitivity / Binding
Can the project work even in principle on such a scale? Would cross-reactivity make a genome wide approach impossible?

- Annemarie Honegger (Zurich) Structural correlates of cross reactivity; libraries
- Wolfgang Hoehne (Berlin) Cross reactivity and polyspecificity; structures
- Paul Predki (Protometrix) Practical cross reactivity in arrays
- Dolores Cahill (Dublin) Practical cross reactivity in arrays
- Ulf Landegren (Uppsala) Solutions to cross reactivity; proximity ligation

10.45 Coffee

11.15 Session 5. Existing applications / alternative techniques / add ons (1)
How does it work so far, how can it be made better?

- Ulf Landegren (Uppsala) Introduction
- Joerg Hoheisel (Heidelberg) Binder arrays: Comparison with DNA chips; selection of antibodies.
- Carl Borrebaeck (Lund) Antibody chips
- Hugues Bedouelle (Paris) Detection techniques, fluorescence

12.45 Lunch in Great Hall

14.15 Session 5. Existing applications / alternative techniques / add ons (2)
- Mike Taussig (Babraham) Protein arrays in situ
- Josh LeBaer (Harvard) Protein arrays: novel approaches
- John McCafferty (Hinxton) Antibodies to profile tissues
- Fredrik Ponten (Uppsala) Tissue arrays
- Olli Kallioneimi (Turku) Comparison with RNAi; cell arrays

16.00 Tea

16.20 Session 6. General Discussion
Whether and how to carry the project forward
Similar initiatives in Europe or USA
How to organise it
How to finance it (EC, industry)

~17.45 Close

19.30 Drinks and dinner at Selwyn College

Thursday 9th Sept

Departure


Participants:

1 Hugues Bedouelle, Institut Pasteur, Paris
2 Carl Borrebaeck, Lund University
3 Andrew Bradbury, Los Alamos
4 Dolores Cahill, RCSI, Dublin
5 Christian Cambillau, CNRS Marseille
6 Ian Dunham, Sanger Institute, Cambridge
7 Mike Dyson, Sanger Insitute, Cambridge
8 Michael Feldhaus, Pacific Northwest National Laboratory, Seattle
9 Paul Ko Ferrigno, Hutchison/MRC research centre, Cambridge
10 Jeremy Gillespie, Invitrogen, Glasgow
11 Larry Gold, Somalogic, Boulder, Colorado
12 Mingyue He, MolTools, Babraham, Cambridge
13 Wolfgang Hoehne, Humboldt University, Berlin
14 Jörg Hoheisel, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg
15 Annemarie Honegger, Dept of Biochemistry, University of Zurich
16 Victor Jongeneel, Ludwig Institute for Cancer Research, Lausanne
17 Farid Khan, MolTools, Babraham, Cambridge
18 Olli-P Kallioniemi, VTT Technical Research Centre, Turku
19 Massoud Kamali-M, MolTools, Rudbeck Laboratory, Uppsala
20 Zoltan Konthur, MolTools, Max Planck Institute for Molecular Biology, Berlin
21 Bernhard Korn, German Genome Resource Centre, RZPD, Heidelberg
22 Urpo Lamminmaki, Dept of Biotechnology, University of Turku
23 Ulf Landegren, Rudbeck Laboratory, Uppsala University
24 Sophie Laurenson, Hutchison/MRC research centre, Cambridge
25 Joshua LeBaer, Harvard Institute of Proteomics, Cambridge (USA)
26 Jim Marks, San Francisco General Hospital
27 Federico de Masi, EMBL, Heidelberg
28 John McCafferty, Sanger Institute, Cambridge
29 Serge Muyldermans, Vrije Universiteit, Brussels
30 Per Ake Nygren, Royal Institute of Technology, Stockholm
31 Nelly Papin, MolTools, CNG, Paris
32 Mathias Paschke, Charite Medical School, Berlin
33 Andreas Plückthun, Biochemisches Institut, Zurich University
34 Fredrik Ponten, Rudbeck Laboratory, Uppsala University
35 Paul Predki, Protometrix, Branford, Connecticut
36 Timo Pulli, MolTools, DKFZ, Heidelberg
37 Carolina Rydin, MolTools administrator, Rudbeck Laboratory, Uppsala
38 Sascha Sauer, MolTools, Max Planck Institute for Molecular Biology, Berlin
39 Edith Schallmeiner, MolTools, Rudbeck Laboratory, Uppsala University
40 Steffen Schlehuber, Pieris Proteolab AG, Freising
41 Cheryl Smythe, ESF coordinator, Babraham, Cambridge
42 Mike Taussig, Babraham, Cambridge
43 Jean-Jacques Toulme, Institut Européen de Chimie et Biologie, Bordeaux
44 Marius Ueffing, GSF, Neuherberg (or representative)
45 Mathias Uhlen, Royal Institute for Biotechnology, Stockholm
46 Martin Yuille, GeneExpress, Cambridge

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