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Gromov P, Celis JE, Gromova I, Rank F, Timmermans-Wielenga V, Moreira JMA. A single lysis solution for the analysis of tissue samples by different proteomic technologies. Mol Oncol 2008; 2:368-79. [PMID: 19383358 DOI: 10.1016/j.molonc.2008.09.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Revised: 09/17/2008] [Accepted: 09/17/2008] [Indexed: 01/20/2023] Open
Abstract
Cancer, being a major healthcare concern worldwide, is one of the main targets for the application of emerging proteomic technologies and these tools promise to revolutionize the way cancer will be diagnosed and treated in the near future. Today, as a result of the unprecedented advances that have taken place in molecular biology, cell biology and genomics there is a pressing need to accelerate the translation of basic discoveries into clinical applications. This need, compounded by mounting evidence that cellular model systems are unable to fully recapitulate all biological aspects of human dissease, is driving scientists to increasingly use clinically relevant samples for biomarker and target discovery. Tissues are heterogeneous and as a result optimization of sample preparation is critical for generating accurate, representative, and highly reproducible quantitative data. Although a large number of protocols for preparation of tissue lysates has been published, so far no single recipe is able to provide a "one-size fits all" solubilization procedure that can be used to analyse the same lysate using different proteomics technologies. Here we present evidence showing that cell lysis buffer 1 (CLB1), a lysis solution commercialized by Zeptosens [a division of Bayer (Schweiz) AG], provides excellent sample solubilization and very high 2D PAGE protein resolution both when using carrier ampholytes and immobilized pH gradient strips. Moreover, this buffer can also be used for array-based proteomics (reverse-phase lysate arrays or direct antibody arrays), allowing the direct comparison of qualitative and quantitative data yielded by these technologies when applied to the same samples. The usefulness of the CLB1 solution for gel-based proteomics was further established by 2D PAGE analysis of a number of technically demanding specimens such as breast carcinoma core needle biopsies and problematic tissues such as brain cortex, cerebellum, skeletal muscle, kidney cortex and tongue. This solution when combined with a specific sample preparation technique - cryostat sectioning of frozen specimens - simplifies tissue sample preparation and solves most of the difficulties associated with the integration of data generated by different proteomic technologies.
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Affiliation(s)
- Pavel Gromov
- Institute of Cancer Biology, Danish Cancer Society, Copenhagen, Denmark.
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VanMeter AJ, Rodriguez AS, Bowman ED, Jen J, Harris CC, Deng J, Calvert VS, Silvestri A, Fredolini C, Chandhoke V, Petricoin EF, Liotta LA, Espina V. Laser capture microdissection and protein microarray analysis of human non-small cell lung cancer: differential epidermal growth factor receptor (EGPR) phosphorylation events associated with mutated EGFR compared with wild type. Mol Cell Proteomics 2008; 7:1902-24. [PMID: 18687633 DOI: 10.1074/mcp.m800204-mcp200] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Little is known about lung carcinoma epidermal growth factor (EGF) kinase pathway signaling within the context of the tissue microenvironment. We quantitatively profiled the phosphorylation and abundance of signal pathway proteins relevant to the EGF receptor within laser capture microdissected untreated, human non-small cell lung cancer (NSCLC) (n = 25) of known epidermal growth factor receptor (EGFR) tyrosine kinase domain mutation status. We measured six phosphorylation sites on EGFR to evaluate whether EGFR mutation status in vivo was associated with the coordinated phosphorylation of specific multiple phosphorylation sites on the EGFR and downstream proteins. Reverse phase protein array quantitation of NSCLC revealed simultaneous increased phosphorylation of EGFR residues Tyr-1148 (p < 0.044) and Tyr-1068 (p < 0.026) and decreased phosphorylation of EGFR Tyr-1045 (p < 0.002), HER2 Tyr-1248 (p < 0.015), IRS-1 Ser-612 (p < 0.001), and SMAD Ser-465/467 (p < 0.011) across all classes of mutated EGFR patient samples compared with wild type. To explore which subset of correlations was influenced by ligand induction versus an intrinsic phenotype of the EGFR mutants, we profiled the time course of 115 cellular signal proteins for EGF ligand-stimulated (three dosages) NSCLC mutant and wild type cultured cell lines. EGFR mutant cell lines (H1975 L858R) displayed a pattern of EGFR Tyr-1045 and HER2 Tyr-1248 phosphorylation similar to that found in tissue. Persistence of phosphorylation for AKT Ser-473 following ligand stimulation was found for the mutant. These data suggest that a higher proportion of the EGFR mutant carcinoma cells may exhibit activation of the phosphatidylinositol 3-kinase/protein kinase B (AKT)/mammalian target of rapamycin (MTOR) pathway through Tyr-1148 and Tyr-1068 and suppression of IRS-1 Ser-612, altered heterodimerization with ERBB2, reduced response to transforming growth factor beta suppression, and reduced ubiquitination/degradation of the EGFR through EGFR Tyr-1045, thus providing a survival advantage. This is the first comparison of multiple, site-specific phosphoproteins with the EGFR tyrosine kinase domain mutation status in vivo.
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Affiliation(s)
- Amy J VanMeter
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia 20110, USA
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Espina V, Edmiston KH, Heiby M, Pierobon M, Sciro M, Merritt B, Banks S, Deng J, VanMeter AJ, Geho DH, Pastore L, Sennesh J, Petricoin EF, Liotta LA. A portrait of tissue phosphoprotein stability in the clinical tissue procurement process. Mol Cell Proteomics 2008; 7:1998-2018. [PMID: 18667411 DOI: 10.1074/mcp.m700596-mcp200] [Citation(s) in RCA: 173] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Little is known about the preanalytical fluctuations of phosphoproteins during tissue procurement for molecular profiling. This information is crucial to establish guidelines for the reliable measurement of these analytes. To develop phosphoprotein profiles of tissue subjected to the trauma of excision, we measured the fidelity of 53 signal pathway phosphoproteins over time in tissue specimens procured in a community clinical practice. This information provides strategies for potential surrogate markers of stability and the design of phosphoprotein preservative/fixation solutions. Eleven different specimen collection time course experiments revealed augmentation (+/-20% from the time 0 sample) of signal pathway phosphoprotein levels as well as decreases over time independent of tissue type, post-translational modification, and protein subcellular location (tissues included breast, colon, lung, ovary, and uterus (endometrium/myometrium) and metastatic melanoma). Comparison across tissue specimens showed an >20% decrease of protein kinase B (AKT) Ser-473 (p < 0.002) and myristoylated alanine-rich C-kinase substrate protein Ser-152/156 (p < 0.0001) within the first 90-min postexcision. Proteins in apoptotic (cleaved caspase-3 Asp-175 (p < 0.001)), proliferation/survival/hypoxia (IRS-1 Ser-612 (p < 0.0003), AMP-activated protein kinase beta Ser-108 (p < 0.005), ERK Thr-202/Tyr-204 (p < 0.003), and GSK3alphabeta Ser-21/9 (p < 0.01)), and transcription factor pathways (STAT1 Tyr-701 (p < 0.005) and cAMP response element-binding protein Ser-133 (p < 0.01)) showed >20% increases within 90-min postprocurement. Endothelial nitric-oxide synthase Ser-1177 did not change over the time period evaluated with breast or leiomyoma tissue. Treatment with phosphatase or kinase inhibitors alone revealed that tissue kinase pathways are active ex vivo. Combinations of kinase and phosphatase inhibitors appeared to stabilize proteins that exhibited increases in the presence of phosphatase inhibitors alone (ATF-2 Thr-71, SAPK/JNK Thr-183/Tyr-185, STAT1 Tyr-701, JAK1 Tyr-1022/1023, and PAK1/PAK2 Ser-199/204/192/197). This time course study 1) establishes the dynamic nature of specific phosphoproteins in excised tissue, 2) demonstrates augmented phosphorylation in the presence of phosphatase inhibitors, 3) shows that kinase inhibitors block the upsurge in phosphorylation of phosphoproteins, 4) provides a rational strategy for room temperature preservation of proteins, and 5) constitutes a foundation for developing evidence-based tissue procurement guidelines.
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Affiliation(s)
- Virginia Espina
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia 20110, USA.
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59
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Järås K, Tajudin AA, Ressine A, Soukka T, Marko-Varga G, Bjartell A, Malm J, Laurell T, Lilja H. ENSAM: Europium Nanoparticles for Signal Enhancement of Antibody Microarrays on Nanoporous Silicon. J Proteome Res 2008; 7:1308-14. [DOI: 10.1021/pr700591j] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kerstin Järås
- Department of Laboratory Medicine, Division of Clinical Chemistry, Lund University, Malmö University Hospital, Malmö, Sweden, Department of Electrical Measurement, Lund University, Lund, Sweden, Department of Biotechnology, University of Turku, Turku, Finland, Department of Analytical Chemistry, Lund University and AstraZeneca R&D Lund, Lund, Sweden, Department of Clinical Sciences, Division of Urological Cancers, Lund University, Malmö University Hospital, Malmö, Sweden, Departments of Clinical
| | - Asilah Ahmad Tajudin
- Department of Laboratory Medicine, Division of Clinical Chemistry, Lund University, Malmö University Hospital, Malmö, Sweden, Department of Electrical Measurement, Lund University, Lund, Sweden, Department of Biotechnology, University of Turku, Turku, Finland, Department of Analytical Chemistry, Lund University and AstraZeneca R&D Lund, Lund, Sweden, Department of Clinical Sciences, Division of Urological Cancers, Lund University, Malmö University Hospital, Malmö, Sweden, Departments of Clinical
| | - Anton Ressine
- Department of Laboratory Medicine, Division of Clinical Chemistry, Lund University, Malmö University Hospital, Malmö, Sweden, Department of Electrical Measurement, Lund University, Lund, Sweden, Department of Biotechnology, University of Turku, Turku, Finland, Department of Analytical Chemistry, Lund University and AstraZeneca R&D Lund, Lund, Sweden, Department of Clinical Sciences, Division of Urological Cancers, Lund University, Malmö University Hospital, Malmö, Sweden, Departments of Clinical
| | - Tero Soukka
- Department of Laboratory Medicine, Division of Clinical Chemistry, Lund University, Malmö University Hospital, Malmö, Sweden, Department of Electrical Measurement, Lund University, Lund, Sweden, Department of Biotechnology, University of Turku, Turku, Finland, Department of Analytical Chemistry, Lund University and AstraZeneca R&D Lund, Lund, Sweden, Department of Clinical Sciences, Division of Urological Cancers, Lund University, Malmö University Hospital, Malmö, Sweden, Departments of Clinical
| | - György Marko-Varga
- Department of Laboratory Medicine, Division of Clinical Chemistry, Lund University, Malmö University Hospital, Malmö, Sweden, Department of Electrical Measurement, Lund University, Lund, Sweden, Department of Biotechnology, University of Turku, Turku, Finland, Department of Analytical Chemistry, Lund University and AstraZeneca R&D Lund, Lund, Sweden, Department of Clinical Sciences, Division of Urological Cancers, Lund University, Malmö University Hospital, Malmö, Sweden, Departments of Clinical
| | - Anders Bjartell
- Department of Laboratory Medicine, Division of Clinical Chemistry, Lund University, Malmö University Hospital, Malmö, Sweden, Department of Electrical Measurement, Lund University, Lund, Sweden, Department of Biotechnology, University of Turku, Turku, Finland, Department of Analytical Chemistry, Lund University and AstraZeneca R&D Lund, Lund, Sweden, Department of Clinical Sciences, Division of Urological Cancers, Lund University, Malmö University Hospital, Malmö, Sweden, Departments of Clinical
| | - Johan Malm
- Department of Laboratory Medicine, Division of Clinical Chemistry, Lund University, Malmö University Hospital, Malmö, Sweden, Department of Electrical Measurement, Lund University, Lund, Sweden, Department of Biotechnology, University of Turku, Turku, Finland, Department of Analytical Chemistry, Lund University and AstraZeneca R&D Lund, Lund, Sweden, Department of Clinical Sciences, Division of Urological Cancers, Lund University, Malmö University Hospital, Malmö, Sweden, Departments of Clinical
| | - Thomas Laurell
- Department of Laboratory Medicine, Division of Clinical Chemistry, Lund University, Malmö University Hospital, Malmö, Sweden, Department of Electrical Measurement, Lund University, Lund, Sweden, Department of Biotechnology, University of Turku, Turku, Finland, Department of Analytical Chemistry, Lund University and AstraZeneca R&D Lund, Lund, Sweden, Department of Clinical Sciences, Division of Urological Cancers, Lund University, Malmö University Hospital, Malmö, Sweden, Departments of Clinical
| | - Hans Lilja
- Department of Laboratory Medicine, Division of Clinical Chemistry, Lund University, Malmö University Hospital, Malmö, Sweden, Department of Electrical Measurement, Lund University, Lund, Sweden, Department of Biotechnology, University of Turku, Turku, Finland, Department of Analytical Chemistry, Lund University and AstraZeneca R&D Lund, Lund, Sweden, Department of Clinical Sciences, Division of Urological Cancers, Lund University, Malmö University Hospital, Malmö, Sweden, Departments of Clinical
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