Development of multiplexed protein profiling and detection using near infrared detection of reverse-phase protein microarrays

Valerie Calvert1, Yihui Tang2, Vince R. Boveia2, Julie Wulfkuhle3, Amy Schutz-Geschwender2, D. Michael Olive2, Lance A. Liotta3, Emanuel F. Petricoin1
1Office of Cell and Gene Therapy, Center for Biologics Evaluation and Research, Food and Drug Administration, NCI/FDA Clinical Proteomics Program, Bethesda
2LI-COR Biosciences, Lincoln
3Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, NCI/FDA Clinical Proteomics Program, Bethesda

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Liotta L, Petricoin E. Molecular profiling of human cancer. Nat Rev Genet 2000;1:48–56.

Ideker T, Thorsson V, Ranish JA, et al. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 2001;292:929–934.

Schwikowski B, Uetz P. Fields S. A network of protein-protein interactions in yeast. Nat Biotechnol 2000;18: 1257–1261.

Legrain P, Jestin JL, Schachter V. From the analysis of protein complexes to proteome-wide linkage maps. Curr Opin Biotechnol 2000;11:402–407.

Blume-Jensen P, Hunter T. Oncogenic kinase signaling. Nature Insight. Cancer 2001;411:355–365.

Pawson T. Protein modules and signaling networks. Nature 1995;373:573–580.

Liotta LA, Kohn EC. The microenvironment of the tumour-host interface. Nature 2001;411:375–379.

Gorg A, Obermaier C, Boguth G, et al. The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 2000;21:1037–1053.

Hanash SM. Biomedical applications of twodimensional electrophoresis using immobilized pH gradients: current status. Electrophoresis 2000;21:1202–1209.

Li J, Wang C, Kelly JF, Harrison DJ, Thibault P. Rapid and sensitive separation of trace level protein digests using microfabricated devices coupled to a quadrupole-time-of-flight mass spectrometer. Electrophoresis 2000;21:198–210.

Gygi SP, Rist B, Geber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex protein mixtures using isotope coded affinity tags. Nature Biotechnol. 1999;17:994–999.

Washburn MP, Wolters D, Yates JR. Large scale analysis of the yeast proteome by multidi-mensional protein identification technology. Nature Biotechnol. 2001;19:242–247.

Krutchinsky, AN, Kalkum M, Chait BT. Automatic identification of proteins with a MALDI-quadrupole ion trap mass spectrometer. Anal Chem 2001;73:5066–5077.

Washburn MP, Ulaszek R, Deciu C, Schieltz DM, Yates JR, III. Analysis of quantitative proteomic data generated via multidimensional protein identification technology. Anal Chem 2002;74:1650–1657.

Zhou H, Ranish JA, Watts JD, Aebersold R. Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry. Nature Biotechnol 2002;20:512–515.

Zhou G, Li H, DeCamp D, et al. 2-D differential in-Gel electrophoresis for the identification of human esophageal squamous cell cancer specific protein markers. Mol Cell Proteomics 2002;1:117–123.

Paweletz CP, Charboneau L, Bichsel VE, et al. Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front. Oncogene 2001;20:1981–1989.

Nishizuka S, Charboneau L, Young L, et al. Diagnostic markers that distinguish colon and ovarian adenocarcinomas: Identification by genomic, proteomic, and tissue array profiling. Cancer Res 2003;63:5173–5646.

Espina V, Mehta AI, Winters ME, Wulfkuhle J, Petricoin III E, Liotta L. Protein microarrays: molecular profiling technologies for clinical specimens. Proteomics 2003;3(11):2091–2100.

Grubb RL, Calvert VS, Paweletz CP, et al. Signal pathway profiling of prostate cancer using reverse phase protein arrays. Proteomics 2003;3(11):2142–6.

Wulfkuhle JD, Aquino JA, Calvert VS, et al. Signal pathway profiling of ovarian cancer from human tissue specimens using vererse-phase microarrays. Proteomics 2003;3(11):2085–90.

Herrmann PC, Gillespie J.W., Charboneau L, et al. Mitochondrial Proteome: Altered Cytochrome Oxidase Subunit Levels in Prostate Cancer. Proteomics 2003;3(9):1801–1810.

Liotta LA, Espina V, Mehta AI, et al. Protein microarrays: Meeting analytical challenges for clinical applications. Cancer Cell 2003;3(4): 317–25.

Petricoin EF, Zoon KC, Kohn EC, Barrett JC, Liotta LA. Clinical Proteomics: Translating Benchside Promise into Bedside Reality. Nature Rev Drug Disc 2002;1:683–695.

Bray D. Molecular networks: the top-down view. Science 2003;301:1864–1865.

Leyland-Jones B. Trastuzumab: hopes and realities. Lancet Oncol 2002;3:137–144.

Sebolt-Leopold JS. Development of anticancer drugs targeting the MAP kinase pathway. Oncogene 2000;19:6594–6599.

Thiesing JT, Ohno-Jones S, Kolibaba KS, Druker B. Efficacy of STI571, an abl tyrosine kinase inhibitor, in conjuction with other antileukemic agents against bcr-abl-positive cells. Blood 2000;96:3195–3199.

Vlahos CJ, Stancato LF. Inhibitors of cellular signaling targets-designs and limitations. Platelets and Megakaryoctyes: Methods and Protocols. In: Gibbons, JM and Mahaut-Smith MP, eds. Humana Press, Totowa, NJ:2002.

Traxler P, Bold G, Buchdunger E, et al. Tyrosine kinase inhibitors: from rational design to clinical trials. Med Res Rev 2001;21:499–512.

Zwick E, Bange J, Ullrich A. Receptor tyrosine kinases as targets for anticancer drugs. Trends Mol Med 2001;8:17–23.

Torhorst J, Bucher C, Kononen J, et al. Tissue microarrays for rapid linking of molecular changes to clinical endpoints. Am J Pathol 2001;159:2249–2256.

Sreekumar A, Nyati MK, Varambally S, et al. Profiling of cancer cells using protein microarrays: discovery of novel radiation-regulated proteins. Cancer Res 2001;61:7585–7593.

MacBeath G. Proteomics comes to the surface. Nature Biotechnol 2001;19:828–829.

Walter G, Bussow K, Lueking A, Glokler J. High-throughput protein arrays: prospects for molecular diagnostics. Trends Mol Med 2002; 8:250–253.

Kuruvilla FG, Shamji AF, Sternson SM, Hergenrother PJ, Schreiber SL. Dissecting glucose signalling with diversity-oriented synthesis and small-molecule microarrays. Nature 2002; 416:653–657.

Liotta LA, Kohn EC, Petricoin EF. Clinical proteomics: personalized molecular medicine. JAMA 2001;286:2211–2214.

Petricoin EF, Zoon KC, Kohn EC, Barrett JC, Liotta LA. Clinical Proteomics: Translating Benchside Promise into Bedside Reality. Nature Rev Drug Disc 2002;1:683–695.