title: Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays.
abstract: Because most potential molecular markers and targets are proteins, proteomic profiling is expected to yield more direct answers to functional and pharmacological questions than does transcriptional profiling. To aid in such studies, we have developed a protocol for making reverse-phase protein lysate microarrays with larger numbers of spots than previously feasible. Our first application of these arrays was to profiling of the 60 human cancer cell lines (NCI-60) used by the National Cancer Institute to screen compounds for anticancer activity. Each glass slide microarray included 648 lysate spots representing the NCI-60 cell lines plus controls, each at 10 two-fold serial dilutions to provide a wide dynamic range. Mouse monoclonal antibodies and the catalyzed signal amplification system were used for immunoquantitation. The signal levels from the >30,000 data points for our first 52 antibodies were analyzed by using p-scan and a quantitative dose interpolation method. Clustered image maps revealed biologically interpretable patterns of protein expression. Among the principal early findings from these arrays were two promising pathological markers for distinguishing colon from ovarian adenocarcinomas. When we compared the patterns of protein expression with those we had obtained for the same genes at the mRNA level by using both cDNA and oligonucleotide arrays, a striking regularity appeared: cell-structure-related proteins almost invariably showed a high correlation between mRNA and protein levels across the NCI-60 cell lines, whereas non-cell-structure-related proteins showed poor correlation.
authors: Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
authors: Satoshi
authors: S
authors: Nishizuka
authors: Lu
authors: L
authors: Charboneau
authors: Lynn
authors: L
authors: Young
authors: Sylvia
authors: S
authors: Major
authors: William C
authors: WC
authors: Reinhold
authors: Mark
authors: M
authors: Waltham
authors: Hosein
authors: H
authors: Kouros-Mehr
authors: Kimberly J
authors: KJ
authors: Bussey
authors: Jae K
authors: JK
authors: Lee
authors: Virginia
authors: V
authors: Espina
authors: Peter J
authors: PJ
authors: Munson
authors: Emanuel
authors: E
authors: Petricoin
authors: Lance A
authors: LA
authors: Liotta
authors: John N
authors: JN
authors: Weinstein
mesh_terms: D015153:Blotting, Western; D045744:Cell Line, Tumor; D004354:Drug Screening Assays, Antitumor / Q000379:methods / Q000706:statistics & numerical data; D005260:Female; D020869:Gene Expression Profiling; D006801:Humans; D008297:Male; D009363:Neoplasm Proteins / Q000235:genetics; D040081:Protein Array Analysis / Q000379:methods* / Q000706:statistics & numerical data; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results
chemical_list: D009363:Neoplasm Proteins