title: Large-scale protein profiling in human cell lines using antibody-based proteomics.
abstract: 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 ( www.proteinatlas.org ), that are of potential use in cell line studies.
authors: Department of Proteomics, School of Biotechnology, AlbaNova University Center, KTH-Royal Institute of Technology, SE-10691 Stockholm, Sweden.
authors: Linn
authors: L
authors: Fagerberg
authors: Sara
authors: S
authors: Strömberg
authors: Adila
authors: A
authors: El-Obeid
authors: Marcus
authors: M
authors: Gry
authors: Kenneth
authors: K
authors: Nilsson
authors: Mathias
authors: M
authors: Uhlen
authors: Fredrik
authors: F
authors: Ponten
authors: Anna
authors: A
authors: Asplund
mesh_terms: D045744:Cell Line, Tumor; D016000:Cluster Analysis; D030562:Databases, Protein; D006801:Humans; D007150:Immunohistochemistry / Q000379:methods*; D009369:Neoplasms / Q000737:chemistry / Q000378:metabolism; D025341:Principal Component Analysis; D011506:Proteins / Q000032:analysis* / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D046888:Tissue Array Analysis / Q000379:methods*
chemical_list: D011506:Proteins