UPPSALA UNIVERSITY : UCG : Members : Fredrik Ponten
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Fredrik Ponten

Department of Genetics and Pathology, Uppsala University. Home Page


Previous research has been morphology-based and focused on skin cancer as a model for carcinogenesis. Developed strategies have included biobanking, immunohistochemistry, microdissection, single cell PCR and array technologies.
Since 2003 FP is site director in Uppsala for the Swedish Human Proteome Resource project (HPR). The HPR project, which is headed by Prof. Mathias Uhlen, Biotechnology, Royal Institute of Technology, Stockholm, involves a large-scale effort to do antibody-based human tissue proteomics. The project, which is funded by the Knut and Alice Wallenberg Foundation (non-profit), commenced July 2003. The aim of this project is to generate specific antibodies towards human gene products and to use these to map expression in human tissues and cells. The HPR project involves two sites, KTH in Stockholm and Rudbeck laboratory in Uppsala. At the Stockholm site mono-specific antibodies (msAb) are generated and in brief methods include: bioinformatic tools to define unique protein epitope signature tags (PrEST); molecular biological tools for efficient cloning; a protein factory for generation and purification of recombinant proteins; strategies for stringent affinity purification of polyclonal antibodies and quality controls using protein arrays. At the Uppsala site the produced msAbs are used for immunohistochemistry on tissue microarrays (TMAs) to screen for expression profiles in various normal and diseased tissues as well as in a large amount of cell lines. All antibodies are screened on > 700 spots including approx. 50 normal tissues, 20 common forms of cancer and 50 cell lines. All immunostained spots are scanned to produce high-quality images. Pathologists using specially designed software for annotation analyze protein expression patterns for tissue profiling. Cell lines are annotated using image analysis tools. All data is stored in a web-based which will be public ally available.

Five Selected Publications

Mathias Uhlen and Fredrik Ponten. Antibody-based proteomics for human tissue profiling. MCP published February 8, 2005, 10.1074/mcp.R500009-MCP200

Caroline Kampf, Ann-Catrin Andersson, Kenneth Wester, Erik Björling, Mathias Uhlen, Fredrik Ponten. Antibody-based Tissue Profiling as a Tool for Clinical Proteomics. Clinical Proteomics, In Press 2005

Peter Nilsson, Linda Paavilainen, Karin Larsson, Jenny Ödling, Mårten Sundberg, Ann-Catrin Andersson, Caroline Kampf, Anja Persson, Cristina Al-Khalili Szigyarto, Jenny Ottosson, Erik Björling, Sophia Hober, Henrik Wernérus, Kenneth Wester, Fredrik Ponten and Mathias Uhlen. Towards a human proteome atlas: high-throughput generation of mono-specific antibodies for tissue profiling. Proteomics, In Press 2005

Agaton C, Galli J, Hoiden Guthenberg I, Janzon L, Hansson M, Asplund A, Brundell E, Lindberg S, Ruthberg I, Wester K, Wurtz D, Hoog C, Lundeberg J, Stahl S, Ponten F, Uhlen M. Affinity proteomics for systematic protein profiling of chromosome 21 gene products in human tissues. Mol Cell Proteomics. 2003 Jun;2(6):405-14. Epub 2003 Jun 09.

F. Ponten & J. Lundeberg. Principles of tumor biology and pathogenesis of BCCs and SCCs. Dermatology, Mosby, Elsivier Ltd. ISBN 0 32302 4092 pp 1663-76 (2003).