Petricoin and Liotta have several irons in the proteomics fire, but the use of Ciphergen's proteinchips has been one of them. Although proteinchips can be put together and read as a 96 well plate, they seem to be developing an alternative. Edited by a guy from SomaLogic, which is a CIPH competitor if memory serves correctly . . .
>>Published online before print November 17, 2003
Proc. Natl. Acad. Sci. USA, 10.1073/pnas.2331323100
Medical Sciences
Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays
Satoshi Nishizuka *, Lu Charboneau , Lynn Young , Sylvia Major *, William C. Reinhold *, Mark Waltham *, Hosein Kouros-Mehr *¶, Kimberly J. Bussey *, Jae K. Lee ||, Virginia Espina , Peter J. Munson , Emanuel Petricoin III **, Lance A. Liotta , and John N. Weinstein *
*Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, Laboratory of Pathology, National Cancer Institute, and Mathematical and Statistical Computing Laboratory, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892; ||Department of Health Evaluation Sciences, P.O. Box 800717, University of Virginia School of Medicine, Charlottesville, VA 22908; and **Tissue Proteomics Unit, Division of Therapeutic Proteins, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD 20892
Edited by Larry Gold, SomaLogic, Inc., Boulder, CO, and approved September 24, 2003 (received for review March 6, 2003)
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.<<
Cheers, Tuck |
