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Large-Scale Protein Profiling in Human Cell Lines Using Antibody-Based Proteomics
KTH, School of Biotechnology (BIO), Proteomics.ORCID iD: 0000-0003-0198-7137
KTH, School of Biotechnology (BIO), Proteomics.
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2011 (English)In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 10, no 9, 4066-4075 p.Article in journal (Refereed) Published
Abstract [en]

Human cancer cell lines grown in vitro are frequently used to decipher basic cell biological phenomena and to also specifically study different forms of cancer. Here we present the first large-scale study of protein expression patterns in cell lines using an antibody-based proteomics approach. We analyzed the expression pattern of 5436 proteins in 45 different cell lines using hierarchical clustering, principal component analysis, and two-group comparisons for the identification of differentially expressed proteins. Our results show that immunohistochemically determined protein profiles can categorize cell lines into groups that overall reflect the tumor tissue of origin and that hematological cell lines appear to retain their protein profiles to a higher degree than cell lines established from solid tumors. The two-group comparisons reveal well-characterized proteins as well as previously unstudied proteins that could be of potential interest for further investigations. Moreover, multiple myeloma cells and cells of myeloid origin were found to share a protein profile, relative to the protein profile of lymphoid leukemia and lymphoma cells, possibly reflecting their common dependency of bone marrow microenvironment. This work also provides an extensive list of antibodies, for which high-resolution images as well as validation data are available on the Human Protein Atlas (, that are of potential use in cell line studies.

Place, publisher, year, edition, pages
2011. Vol. 10, no 9, 4066-4075 p.
Keyword [en]
human cell lines, immunohistochemistry, proteomics, image analysis, hierarchical clustering
National Category
Medical Biotechnology
URN: urn:nbn:se:kth:diva-40659DOI: 10.1021/pr200259vISI: 000294446600019OAI: diva2:443626
Knut and Alice Wallenberg FoundationScience for Life Laboratory - a national resource center for high-throughput molecular bioscience
QC 20110926Available from: 2011-09-26 Created: 2011-09-20 Last updated: 2012-06-18Bibliographically approved

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