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Jan 1, 2009 (Vol. 29, No. 1)

Exploring the Human Proteome in Depth

Need for Extensive and Reliable Identification of Proteins Is Now Widely Recognized

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    Multicolor labeling of breast carcinoma cells for high-content screening

    Screening technologies for proteins are still gaining momentum, and as the discipline matures scientists are wondering what technologies are best suited for proteomic profiling. “There’s also a lot of discussion about quantification methodology—what is the best and most efficient way to get the results you need,” notes Chris Becker, executive director of PPD.

    Additionally, there have been concerns about the maturity of the different proteomic technologies. “Proteomics is a hyped area,” says Christer Wingren, Ph.D., associate professor at the Lund University. “But it’s starting to become a mature platform based on what you can do in clinical and profile studies.”

    In order to address advances in the screening arena, Select Biosciences is hosting three meetings in Berlin next month. A few of the presenters at the “Screening” meeting spoke to GEN before the conferences to explain where protein profiling stands today.

    The Swedish Human Proteome Resource program (HPR) was developed to allow for a systematic exploration of the human proteome using antibody-based proteomics. This research combines high-throughput generation of affinity-purified (mono-specific) antibodies with protein profiling in a multitude of tissue/cell types assembled in tissue microarrays.

    “The program hosts the Human Protein Atlas portal with expression profiles of human proteins in tissues and cells,” explains Frederik Ponten, M.D., Ph.D., department of genetics and pathology, Uppsala University.

    Dr. Ponten’s presentation will describe his group’s multidisciplinary research program, which will allow for systematic exploration of the human proteome using antibody-based tissue proteomics, combining high-throughput generation of mono-specific antibodies (affinity-purified) with protein profiling in human tissues and cells using tissue microarrays.

    “We began this project five years ago on two different sites, Stockholm and Uppsala. Eighty researchers are working on this full time,” notes Dr. Ponten. “We are in a steady state, averaging 20 antibodies a day; 50 percent are approved and work well enough to do protein profiling. It actually boils down to ten antibodies a day or 3,000 new protein profiles a year.

    “A new version of the Human Protein Atlas is released on an annual basis, and the current version contains protein profiles for over 6,000 antibodies representing 5,000 unique human proteins corresponding to 25 percent of the human genome.”

    Dr. Ponten’s group is concentrating on finding predictive biomarkers for cancer, with a focus on major human cancer types including breast, colorectal, prostate, and lung cancer in particular.

    “I hope people recognize us as a resource for protein-related research,” remarks Dr. Ponten. “We need to get the word out that we’re here. The effort is fairly well known in the proteomics community, but in the cancer field, people need to know that we are a resource that can be utilized for various research projects.”

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