Comprehensive proteomic analysis of breast cancer cell membranes reveals unique proteins with potential roles in clinical cancer.
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.
Adam
Paul J
PJ
Oxford Glycosciences, The Forum, 86 Milton Park, Abingdon, Oxford OX14 4RY, United Kingdom.
Boyd
Robert
R
Tyson
Kerry L
KL
Fletcher
Graham C
GC
Stamps
Alasdair
A
Hudson
Lindsey
L
Poyser
Helen R
HR
Redpath
Nick
N
Griffiths
Matthew
M
Steers
Graham
G
Harris
Adrian L
AL
Patel
Sonal
S
Berry
Joanne
J
Loader
Julie A
JA
Townsend
R Reid
RR
Daviet
Laurent
L
Legrain
Pierre
P
Parekh
Raj
R
Terrett
Jonathan A
JA
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
D008565:Membrane Proteins; D009363:Neoplasm Proteins; D010446:Peptide Fragments; D020543:Proteome