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Chromosome 21 pilot

A pilot study was initiated in 2000 to investigate all genes encoded by human chromosome 21. The study is the first chromosome-wide exploration in which an affinity proteomics strategy using antibodies raised against recombinant human protein fragments was used for protein profiling. The results, published in 2003, suggested that this strategy could be used to produce a proteome atlas describing distribution and expression of proteins in normal and disease tissues.

Key publication

  • Agaton C et al., Affinity proteomics for systematic protein profiling of chromosome 21 gene products in human tissues. Mol Cell Proteomics. (2003)
    PubMed: 12796447 DOI: 10.1074/mcp.M300022-MCP200

Other selected publications

  • Gräslund S et al., A high-stringency proteomics concept aimed for generation of antibodies specific for cDNA-encoded proteins. Biotechnol Appl Biochem. (2002)
    PubMed: 11916449 DOI: 10.1042/ba20010097

  • Agaton C et al., Selective enrichment of monospecific polyclonal antibodies for antibody-based proteomics efforts.  J Chromatogr A (2004)
    PubMed: 15317410 

  • Berglund L et al., A whole-genome bioinformatics approach to selection of antigens for systematic antibody generation. Proteomics. (2008)
    PubMed: 18655051 DOI: 10.1002/pmic.200800203

  • UhlĂ©n M et al., Antibody-based protein profiling of the human chromosome 21. Mol Cell Proteomics. (2012)
    PubMed: 22042635 DOI: 10.1074/mcp.M111.013458

Figure legend: The pipeline to generate antibodies and protein profiles corresponding to a majority of the protein-coding genes at human chromosome 21. Bioinformatics tools were used to design recombinant protein fragments with unique epitopes. The recombinant protein fragments were produced using de novo cloning from RNA pools and expression in Escherichia coli. The purified recombinant protein fragments were used to immunize rabbits to generate polyclonal antibodies. The polyclonal antibodies were affinity purified using the recombinant protein fragments as affinity ligands, resulting in target protein-specific antibodies. Protein profiling was performed using tissue microarrays and target-specific polyclonal antibodies, enabling multiscale protein-expression analysis.

Key facts

  • Antibodies to more than half of the proteins encoded by the 225 genes on chromosome 21 were generated
  • The antibodies were used for tissue exploration using immunohistochemistry
  • The success rate of the whole concept, from in silico design to protein profiling, makes the strategy suitable for genome-wide protein profiling