title: Comprehensive proteomic analysis of breast cancer cell membranes reveals unique proteins with potential roles in clinical cancer.
abstract: Proteins associated with cancer cell plasma membranes are rich in known drug and antibody targets as well as other proteins known to play key roles in the abnormal signal transduction processes required for carcinogenesis. We describe here a proteomics process that comprehensively annotates the protein content of breast tumor cell membranes and defines the clinical relevance of such proteins. Tumor-derived cell lines were used to ensure an enrichment for cancer cell-specific plasma membrane proteins because it is difficult to purify cancer cells and then obtain good membrane preparations from clinical material. Multiple cell lines with different molecular pathologies were used to represent the clinical heterogeneity of breast cancer. Peptide tandem mass spectra were searched against a comprehensive data base containing known and conceptual proteins derived from many public data bases including the draft human genome sequences. This plasma membrane-enriched proteome analysis created a data base of more than 500 breast cancer cell line proteins, 27% of which were of unknown function. The value of our approach is demonstrated by further detailed analyses of three previously uncharacterized proteins whose clinical relevance has been defined by their unique cancer expression profiles and the identification of protein-binding partners that elucidate potential functionality in cancer.
authors.affiliation: Oxford Glycosciences, The Forum, 86 Milton Park, Abingdon, Oxford OX14 4RY, United Kingdom.
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Adam
authors.forename: Robert
authors.initials: R
authors.lastname: Boyd
authors.forename: Kerry L
authors.initials: KL
authors.lastname: Tyson
authors.forename: Graham C
authors.initials: GC
authors.lastname: Fletcher
authors.forename: Alasdair
authors.initials: A
authors.lastname: Stamps
authors.forename: Lindsey
authors.initials: L
authors.lastname: Hudson
authors.forename: Helen R
authors.initials: HR
authors.lastname: Poyser
authors.forename: Nick
authors.initials: N
authors.lastname: Redpath
authors.forename: Matthew
authors.initials: M
authors.lastname: Griffiths
authors.forename: Graham
authors.initials: G
authors.lastname: Steers
authors.forename: Adrian L
authors.initials: AL
authors.lastname: Harris
authors.forename: Sonal
authors.initials: S
authors.lastname: Patel
authors.forename: Joanne
authors.initials: J
authors.lastname: Berry
authors.forename: Julie A
authors.initials: JA
authors.lastname: Loader
authors.forename: R Reid
authors.initials: RR
authors.lastname: Townsend
authors.forename: Laurent
authors.initials: L
authors.lastname: Daviet
authors.forename: Pierre
authors.initials: P
authors.lastname: Legrain
authors.forename: Raj
authors.initials: R
authors.lastname: Parekh
authors.forename: Jonathan A
authors.initials: JA
authors.lastname: Terrett
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology; D003001:Cloning, Molecular; D005260:Female; D006801:Humans; D008565:Membrane Proteins / Q000737:chemistry / Q000235:genetics*; D008969:Molecular Sequence Data; D009363:Neoplasm Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D010446:Peptide Fragments / Q000737:chemistry; D016133:Polymerase Chain Reaction; D020543:Proteome / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D014162:Transfection; D014407:Tumor Cells, Cultured
chemical_list: D008565:Membrane Proteins; D009363:Neoplasm Proteins; D010446:Peptide Fragments; D020543:Proteome