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Craig D, Mazilu M, Dholakia K. Quantitative detection of pharmaceuticals using a combination of paper microfluidics and wavelength modulated Raman spectroscopy. PLoS One 2015; 10:e0123334. [PMID: 25938464 PMCID: PMC4418578 DOI: 10.1371/journal.pone.0123334] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 02/20/2015] [Indexed: 12/14/2022] Open
Abstract
Raman spectroscopy has proven to be an indispensable technique for the identification of various types of analytes due to the fingerprint vibration spectrum obtained. Paper microfluidics has also emerged as a low cost, easy to fabricate and portable approach for point of care testing. However, due to inherent background fluorescence, combining Raman spectroscopy with paper microfluidics is to date an unmet challenge in the absence of using surface enhanced mechanisms. We describe the first use of wavelength modulated Raman spectroscopy (WMRS) for analysis on a paper microfluidics platform. This study demonstrates the ability to suppress the background fluorescence of the paper using WMRS and the subsequent implementation of this technique for pharmaceutical analysis. The results of this study demonstrate that it is possible to discriminate between both paracetamol and ibuprofen, whilst, also being able to detect the presence of each analyte quantitatively at nanomolar concentrations.
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Affiliation(s)
- Derek Craig
- University of St. Andrews, Department of Physics and Astronomy, St. Andrews, Fife, United Kingdom
| | - Michael Mazilu
- University of St. Andrews, Department of Physics and Astronomy, St. Andrews, Fife, United Kingdom
| | - Kishan Dholakia
- University of St. Andrews, Department of Physics and Astronomy, St. Andrews, Fife, United Kingdom
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52
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Dittmar G, Selbach M. SILAC for biomarker discovery. Proteomics Clin Appl 2015; 9:301-6. [PMID: 25504673 DOI: 10.1002/prca.201400112] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 11/05/2014] [Accepted: 12/10/2014] [Indexed: 12/22/2022]
Abstract
SILAC has been employed in MS-based proteomics for nearly a decade. This method is based on cells in culture metabolically incorporating isotope-coded essential amino acids and allows the quantification of global protein populations to identify characteristic changes. Variations of this technique developed over the years allow the application of SILAC not only to cell culture derived samples but also to tissues and human specimens, making this powerful technique amenable to clinically relevant samples. In this review, we provide an overview of different SILAC-derived methods and their use in the identification and development of biomarkers.
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Affiliation(s)
- Gunnar Dittmar
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
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53
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Iliuk AB, Arrington JV, Tao WA. Analytical challenges translating mass spectrometry-based phosphoproteomics from discovery to clinical applications. Electrophoresis 2014; 35:3430-40. [PMID: 24890697 PMCID: PMC4250476 DOI: 10.1002/elps.201400153] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 04/29/2014] [Accepted: 05/12/2014] [Indexed: 12/21/2022]
Abstract
Phosphoproteomics is the systematic study of one of the most common protein modifications in high throughput with the aim of providing detailed information of the control, response, and communication of biological systems in health and disease. Advances in analytical technologies and strategies, in particular the contributions of high-resolution mass spectrometers, efficient enrichments of phosphopeptides, and fast data acquisition and annotation, have catalyzed dramatic expansion of signaling landscapes in multiple systems during the past decade. While phosphoproteomics is an essential inquiry to map high-resolution signaling networks and to find relevant events among the apparently ubiquitous and widespread modifications of proteome, it presents tremendous challenges in separation sciences to translate it from discovery to clinical practice. In this mini-review, we summarize the analytical tools currently utilized for phosphoproteomic analysis (with focus on MS), progresses made on deciphering clinically relevant kinase-substrate networks, MS uses for biomarker discovery and validation, and the potential of phosphoproteomics for disease diagnostics and personalized medicine.
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Affiliation(s)
- Anton B. Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | | | - Weiguo Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
- Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, USA
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54
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Yuan K, Wu H, Wang Y, Chen H, Jiao M, Fu R. Phospho-PRAS40 Thr246 predicts trastuzumab response in patients with HER2-positive metastatic breast cancer. Oncol Lett 2014; 9:785-789. [PMID: 25621052 PMCID: PMC4301480 DOI: 10.3892/ol.2014.2744] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 10/22/2014] [Indexed: 11/15/2022] Open
Abstract
Resistance to trastuzumab is frequently observed during the treatment of patients with human epidermal growth factor 2 (HER2)-positive metastatic breast cancers. The aim of the present study was to determine if the phosphorylated proline-rich Akt substrate of 40 kDa (phospho-PRAS40Thr246), a novel biomarker for phosphoinositol-3 kinase (PI3K) pathway activation, could predict the response of HER2-positive metastatic breast cancers to treatment with trastuzumab. Formalin-fixed, paraffin-embedded tumor tissue samples were retrospectively collected from 55 trastuzumab-treated patients. Next, the expression of phospho-PRAS40Thr246 and phosphatase and tensin homolog (PTEN) was assessed by immunohistochemistry. In total, five common phosphoinositol-3 kinase α catalytic subunit mutations, namely E542K, E545K, E545D, H1047R and H1047L, were identified by the amplification-refractory mutation system, using the allele-specific polymerase chain reaction. The activation of the PI3K pathway, as determined by low PTEN expression or the presence of oncogenic PIK3CA mutations, was observed in 49.1% (27 cases) of the 55 HER2-positive metastatic breast cancer tissues. In total, 40% of the tumors were defined as being phospho-PRAS40Thr246-positive. Furthermore, the results revealed that phospho-PRAS40Thr246 expression was associated with the PI3K pathway activation status and an increased risk of tumor progression in HER2-positive metastatic breast cancer patients who had received trastuzumab-based therapy. Therefore, phospho-PRAS40Thr246 expression levels may reflect the PI3K pathway activation status and act as a biomarker for HER2-amplified breast cancer patients who are unlikely to respond to trastuzumab-based therapy.
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Affiliation(s)
- Kai Yuan
- Department of Breast Surgery, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong 250014, P.R. China
| | - Hongyan Wu
- Department of Breast Surgery, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong 250014, P.R. China
| | - Yulong Wang
- Department of Breast Surgery, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong 250014, P.R. China
| | - Hongqiang Chen
- Department of Breast Surgery, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong 250014, P.R. China
| | - Mingwen Jiao
- Department of Breast Surgery, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong 250014, P.R. China
| | - Rongzhan Fu
- Department of Breast Surgery, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong 250014, P.R. China
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55
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Li T, Wang G. Computer-aided targeting of the PI3K/Akt/mTOR pathway: toxicity reduction and therapeutic opportunities. Int J Mol Sci 2014; 15:18856-91. [PMID: 25334061 PMCID: PMC4227251 DOI: 10.3390/ijms151018856] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 09/21/2014] [Accepted: 10/08/2014] [Indexed: 12/14/2022] Open
Abstract
The PI3K/Akt/mTOR pathway plays an essential role in a wide range of biological functions, including metabolism, macromolecular synthesis, cell growth, proliferation and survival. Its versatility, however, makes it a conspicuous target of many pathogens; and the consequential deregulations of this pathway often lead to complications, such as tumorigenesis, type 2 diabetes and cardiovascular diseases. Molecular targeted therapy, aimed at modulating the deregulated pathway, holds great promise for controlling these diseases, though side effects may be inevitable, given the ubiquity of the pathway in cell functions. Here, we review a variety of factors found to modulate the PI3K/Akt/mTOR pathway, including gene mutations, certain metabolites, inflammatory factors, chemical toxicants, drugs found to rectify the pathway, as well as viruses that hijack the pathway for their own synthetic purposes. Furthermore, this evidence of PI3K/Akt/mTOR pathway alteration and related pathogenesis has inspired the exploration of computer-aided targeting of this pathway to optimize therapeutic strategies. Herein, we discuss several possible options, using computer-aided targeting, to reduce the toxicity of molecularly-targeted therapy, including mathematical modeling, to reveal system-level control mechanisms and to confer a low-dosage combination therapy, the potential of PP2A as a therapeutic target, the formulation of parameters to identify patients who would most benefit from specific targeted therapies and molecular dynamics simulations and docking studies to discover drugs that are isoform specific or mutation selective so as to avoid undesired broad inhibitions. We hope this review will stimulate novel ideas for pharmaceutical discovery and deepen our understanding of curability and toxicity by targeting the PI3K/Akt/mTOR pathway.
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Affiliation(s)
- Tan Li
- Department of Biology, South University of Science and Technology of China, 1088 Xueyuan Rd., Shenzhen 518055, China.
| | - Guanyu Wang
- Department of Biology, South University of Science and Technology of China, 1088 Xueyuan Rd., Shenzhen 518055, China.
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56
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Lu Y, Liu C, Xu YF, Cheng H, Shi S, Wu CT, Yu XJ. Stathmin destabilizing microtubule dynamics promotes malignant potential in cancer cells by epithelial-mesenchymal transition. Hepatobiliary Pancreat Dis Int 2014; 13:386-94. [PMID: 25100123 DOI: 10.1016/s1499-3872(14)60038-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Stathmin is a ubiquitous cytosolic regulatory phosphoprotein and is overexpressed in different human malignancies. The main physiological function of stathmin is to interfere with microtubule dynamics by promoting depolymerization of microtubules or by preventing polymerization of tubulin heterodimers. Stathmin plays important roles in regulating many cellular functions as a result of its microtubule-destabilizing activity. Currently, the critical roles of stathmin in cancer cells, as well as in lymphocytes have been valued. This review discusses stathmin and microtubule dynamics in cancer development, and hypothesizes their possible relationship with epithelial-mesenchymal transition (EMT). DATA SOURCES A PubMed search using such terms as "stathmin", "microtubule dynamics", "epithelial-mesenchymal transition", "EMT", "malignant potential" and "cancer" was performed to identify relevant studies published in English. More than 100 related articles were reviewed. RESULTS The literature clearly documented the relationship between stathmin and its microtubule-destabilizing activity of cancer development. However, the particular mechanism is poorly understood. Microtubule disruption is essential for EMT, which is a crucial process during cancer development. As a microtubule-destabilizing protein, stathmin may promote malignant potential in cancer cells by initiating EMT. CONCLUSIONS We propose that there is a stathmin-microtubule dynamics-EMT (S-M-E) axis during cancer development. By this axis, stathmin together with its microtubule-destabilizing activity contributes to EMT, which stimulates the malignant potential in cancer cells.
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Affiliation(s)
- Yu Lu
- Pancreatic Cancer Institute, Fudan University; Department of Pancreatic and Hepatobiliary Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
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57
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Ullal AV, Peterson V, Agasti SS, Tuang S, Juric D, Castro CM, Weissleder R. Cancer cell profiling by barcoding allows multiplexed protein analysis in fine-needle aspirates. Sci Transl Med 2014; 6:219ra9. [PMID: 24431113 DOI: 10.1126/scitranslmed.3007361] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Immunohistochemistry-based clinical diagnoses require invasive core biopsies and use a limited number of protein stains to identify and classify cancers. We introduce a technology that allows analysis of hundreds of proteins from minimally invasive fine-needle aspirates (FNAs), which contain much smaller numbers of cells than core biopsies. The method capitalizes on DNA-barcoded antibody sensing, where barcodes can be photocleaved and digitally detected without any amplification steps. After extensive benchmarking in cell lines, this method showed high reproducibility and achieved single-cell sensitivity. We used this approach to profile ~90 proteins in cells from FNAs and subsequently map patient heterogeneity at the protein level. Additionally, we demonstrate how the method could be used as a clinical tool to identify pathway responses to molecularly targeted drugs and to predict drug response in patient samples. This technique combines specificity with ease of use to offer a new tool for understanding human cancers and designing future clinical trials.
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Affiliation(s)
- Adeeti V Ullal
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge Street, CPZN 5206, Boston, MA 02114, USA
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58
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Shipitsin M, Small C, Giladi E, Siddiqui S, Choudhury S, Hussain S, Huang YE, Chang H, Rimm DL, Berman DM, Nifong TP, Blume-Jensen P. Automated quantitative multiplex immunofluorescence in situ imaging identifies phospho-S6 and phospho-PRAS40 as predictive protein biomarkers for prostate cancer lethality. Proteome Sci 2014; 12:40. [PMID: 25075204 PMCID: PMC4114438 DOI: 10.1186/1477-5956-12-40] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 06/18/2014] [Indexed: 11/10/2022] Open
Abstract
Background We have witnessed significant progress in gene-based approaches to cancer prognostication, promising early intervention for high-risk patients and avoidance of overtreatment for low-risk patients. However, there has been less advancement in protein-based approaches, even though perturbed protein levels and post-translational modifications are more directly linked with phenotype. Most current, gene expression-based platforms require tissue lysis resulting in loss of structural and molecular information, and hence are blind to tumor heterogeneity and morphological features. Results Here we report an automated, integrated multiplex immunofluorescence in situ imaging approach that quantitatively measures protein biomarker levels and activity states in defined intact tissue regions where the biomarkers of interest exert their phenotype. Using this approach, we confirm that four previously reported prognostic markers, PTEN, SMAD4, CCND1 and SPP1, can predict lethal outcome of human prostate cancer. Furthermore, we show that two PI3K pathway-regulated protein activities, pS6 (RPS6-phosphoserines 235/236) and pPRAS40 (AKT1S1-phosphothreonine 246), correlate with prostate cancer lethal outcome as well (individual marker hazard ratios of 2.04 and 2.03, respectively). Finally, we incorporate these 2 markers into a novel 5-marker protein signature, SMAD4, CCND1, SPP1, pS6, and pPRAS40, which is highly predictive for prostate cancer-specific death. The ability to substitute PTEN with phospho-markers demonstrates the potential of quantitative protein activity state measurements on intact tissue. Conclusions In summary, our approach can reproducibly and simultaneously quantify and assess multiple protein levels and functional activities on intact tissue specimens. We believe it is broadly applicable to not only cancer but other diseases, and propose that it should be well suited for prognostication at early stages of pathogenesis where key signaling protein levels and activities are perturbed.
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Affiliation(s)
| | | | - Eldar Giladi
- Metamark Genetics Inc, Cambridge, MA, USA ; Current address: Atreca, San Carlos, CA, USA
| | - Summar Siddiqui
- Metamark Genetics Inc, Cambridge, MA, USA ; Current address: Moderna, Cambridge, MA, USA
| | | | | | - Yi E Huang
- Metamark Genetics Inc, Cambridge, MA, USA
| | - Hua Chang
- Metamark Genetics Inc, Cambridge, MA, USA
| | - David L Rimm
- Department of Pathology, Yale University Medical School, New Haven, CT, USA
| | - David M Berman
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | | | - Peter Blume-Jensen
- Metamark Genetics Inc, Cambridge, MA, USA ; Current address: XTuit Pharmaceuticals, Inc, Cambridge, MA, USA
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59
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Giri K, Shameer K, Zimmermann M, Saha S, Chakraborty PK, Sharma A, Arvizo RR, Madden BJ, Mccormick DJ, Kocher JPA, Bhattacharya R, Mukherjee P. Understanding protein-nanoparticle interaction: a new gateway to disease therapeutics. Bioconjug Chem 2014; 25:1078-90. [PMID: 24831101 PMCID: PMC4128259 DOI: 10.1021/bc500084f] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 05/14/2014] [Indexed: 02/08/2023]
Abstract
Molecular identification of protein molecules surrounding nanoparticles (NPs) may provide useful information that influences NP clearance, biodistribution, and toxicity. Hence, nanoproteomics provides specific information about the environment that NPs interact with and can therefore report on the changes in protein distribution that occurs during tumorigenesis. Therefore, we hypothesized that characterization and identification of protein molecules that interact with 20 nm AuNPs from cancer and noncancer cells may provide mechanistic insights into the biology of tumor growth and metastasis and identify new therapeutic targets in ovarian cancer. Hence, in the present study, we systematically examined the interaction of the protein molecules with 20 nm AuNPs from cancer and noncancerous cell lysates. Time-resolved proteomic profiles of NP-protein complexes demonstrated electrostatic interaction to be the governing factor in the initial time-points which are dominated by further stabilization interaction at longer time-points as determined by ultraviolet-visible spectroscopy (UV-vis), dynamic light scattering (DLS), ζ-potential measurements, transmission electron microscopy (TEM), and tandem mass spectrometry (MS/MS). Reduction in size, charge, and number of bound proteins were observed as the protein-NP complex stabilized over time. Interestingly, proteins related to mRNA processing were overwhelmingly represented on the NP-protein complex at all times. More importantly, comparative proteomic analyses revealed enrichment of a number of cancer-specific proteins on the AuNP surface. Network analyses of these proteins highlighted important hub nodes that could potentially be targeted for maximal therapeutic advantage in the treatment of ovarian cancer. The importance of this methodology and the biological significance of the network proteins were validated by a functional study of three hubs that exhibited variable connectivity, namely, PPA1, SMNDC1, and PI15. Western blot analysis revealed overexpression of these proteins in ovarian cancer cells when compared to normal cells. Silencing of PPA1, SMNDC1, and PI15 by the siRNA approach significantly inhibited proliferation of ovarian cancer cells and the effect correlated with the connectivity pattern obtained from our network analyses.
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Affiliation(s)
- Karuna Giri
- Department of Biochemistry and Molecular Biology, Division of Biomedical Statistics
and Informatics, Department of Health Sciences Research, Molecular Medicine
Program, and Proteomics
Research Center, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Khader Shameer
- Department of Biochemistry and Molecular Biology, Division of Biomedical Statistics
and Informatics, Department of Health Sciences Research, Molecular Medicine
Program, and Proteomics
Research Center, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Michael
T. Zimmermann
- Department of Biochemistry and Molecular Biology, Division of Biomedical Statistics
and Informatics, Department of Health Sciences Research, Molecular Medicine
Program, and Proteomics
Research Center, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Sounik Saha
- Stanton
L. Young Biomedical Research Center, University
of Oklahoma Health Science Center, Oklahoma City, Oklahoma 73104, United States
| | - Prabir K. Chakraborty
- Stanton
L. Young Biomedical Research Center, University
of Oklahoma Health Science Center, Oklahoma City, Oklahoma 73104, United States
| | - Anirudh Sharma
- Department
of Biomedical Engineering, The University
of Texas, Austin, Texas 78712, United
States
| | - Rochelle R. Arvizo
- Department of Biochemistry and Molecular Biology, Division of Biomedical Statistics
and Informatics, Department of Health Sciences Research, Molecular Medicine
Program, and Proteomics
Research Center, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Benjamin J. Madden
- Department of Biochemistry and Molecular Biology, Division of Biomedical Statistics
and Informatics, Department of Health Sciences Research, Molecular Medicine
Program, and Proteomics
Research Center, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Daniel J. Mccormick
- Department of Biochemistry and Molecular Biology, Division of Biomedical Statistics
and Informatics, Department of Health Sciences Research, Molecular Medicine
Program, and Proteomics
Research Center, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Jean-Pierre A. Kocher
- Department of Biochemistry and Molecular Biology, Division of Biomedical Statistics
and Informatics, Department of Health Sciences Research, Molecular Medicine
Program, and Proteomics
Research Center, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Resham Bhattacharya
- Stanton
L. Young Biomedical Research Center, University
of Oklahoma Health Science Center, Oklahoma City, Oklahoma 73104, United States
| | - Priyabrata Mukherjee
- Stanton
L. Young Biomedical Research Center, University
of Oklahoma Health Science Center, Oklahoma City, Oklahoma 73104, United States
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60
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Kwong LN, Davies MA. Navigating the therapeutic complexity of PI3K pathway inhibition in melanoma. Clin Cancer Res 2014; 19:5310-9. [PMID: 24089444 DOI: 10.1158/1078-0432.ccr-13-0142] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Melanoma is entering into an era of combinatorial approaches to build upon recent clinical breakthroughs achieved by novel single-agent therapies. One of the leading targets to emerge from the growing understanding of the molecular pathogenesis, heterogeneity, and resistance mechanisms of melanomas is the phosphoinositide 3-kinase (PI3K)-AKT pathway. Multiple genetic and epigenetic aberrations that activate this pathway have been identified in melanomas de novo and in acquired resistance models. These developments have been paralleled by the establishment of models for preclinical testing and the availability of compounds that target various effectors in the pathway. Thus, in addition to having a strong rationale for targeting, the PI3K-AKT pathway presents an immediate clinical opportunity. However, the development of effective strategies against this pathway must overcome several key challenges, including optimizing patient selection, overcoming feedback loops, and pathway cross-talk that can mediate resistance. This review discusses the current understanding and ongoing research about the PI3K-AKT pathway in melanoma and emerging strategies to achieve clinical benefit in patients by targeting it.
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Affiliation(s)
- Lawrence N Kwong
- Authors' Affiliations: Departments of Genomic Medicine, Melanoma Medical Oncology, and Systems Biology, University of Texas MD Anderson Cancer Center, Houston, Texas
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61
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Havel JJ, Li Z, Cheng D, Peng J, Fu H. Nuclear PRAS40 couples the Akt/mTORC1 signaling axis to the RPL11-HDM2-p53 nucleolar stress response pathway. Oncogene 2014; 34:1487-98. [PMID: 24704832 PMCID: PMC4216640 DOI: 10.1038/onc.2014.91] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Revised: 02/26/2014] [Accepted: 03/01/2014] [Indexed: 12/27/2022]
Abstract
The Ribosomal Protein (RP)-HDM2-p53 pathway has been shown to play key roles in oncogene-induced apoptosis and senescence, but the mechanism regulating this pathway remains elusive. The Proline-Rich Akt Substrate of 40 kDA (PRAS40) has recently been identified as a binding partner and inhibitor of the mechanistic Target of Rapamycin Complex 1 (mTORC1). Although other inhibitors of mTORC1 are known tumor suppressors, PRAS40 promotes cell survival and tumorigenesis. Here we demonstrate that Akt- and mTORC1-mediated phosphorylation of PRAS40 at T246 and S221, respectively, promotes nuclear-specific association of PRAS40 with Ribosomal Protein L11 (RPL11). Importantly, silencing of PRAS40 induces upregulation of p53 in a manner dependent upon RPL11. This effect is rescued by wild type PRAS40, but not by the RPL11 binding-null PRAS40 T246A mutant. We find that PRAS40 negatively regulates the RPL11-HDM2-p53 nucleolar stress response pathway and suppresses induction of p53-mediated cellular senescence. This work identifies nuclear PRAS40 as a dual-input signaling checkpoint that links cell growth and proliferation to inhibition of cellular senescence. These findings may help to explain the pro-tumorigenic effect of PRAS40 and identify the PRAS40-RPL11 complex as a promising target for p53-restorative anti-cancer drug discovery.
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Affiliation(s)
- J J Havel
- 1] Department of Pharmacology, Emory University School of Medicine, Atlanta, GA, USA [2] Graduate Program in Molecular and Systems Pharmacology, Emory University, Atlanta, GA, USA
| | - Z Li
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA, USA
| | - D Cheng
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - J Peng
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - H Fu
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA, USA
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62
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Lu YZ, Deng AM, Li LH, Liu GY, Wu GY. Prognostic role of phospho-PRAS40 (Thr246) expression in gastric cancer. Arch Med Sci 2014; 10:149-53. [PMID: 24701227 PMCID: PMC3953967 DOI: 10.5114/aoms.2013.36927] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 11/18/2011] [Accepted: 12/14/2011] [Indexed: 12/21/2022] Open
Abstract
INTRODUCTIONS Phospho-PRAS40(Thr246) (phosphorylated proline-rich Akt substrate of 40 kilodaltons at Thr246) is a biomarker for phosphatidylinositol 3-kinase (PI3K) pathway activation and AKT inhibitors sensitivity. MATERIAL AND METHODS In this study, we immunohistochemically investigated the expression of phospho-PRAS40(Thr246) in 141 gastric cancer tumors, and evaluated its clinicopathological and prognostic significance. RESULTS Sixty-four cases (45.4%) were defined as phospho-PRAS40(Thr246) positive. Phospho-PRAS40(Thr246) correlated positively with lymph node metastasis, lymphatic infiltration, vascular infiltration and shorter survival. Furthermore, phospho-PRAS40(Thr246) is an independent prognostic factor for gastric cancer. CONCLUSIONS Our data suggest that phospho-PRAS40(Thr246) was frequently expressed in gastric cancers, and correlated with malignant progression and poor prognosis of patients. PI3K pathway-targeted therapies should be considered in the future treatment of gastric cancers.
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Affiliation(s)
- Yi-Zhuo Lu
- Department of General Surgery, Zhongshan Hospital, Research Institute of Digestive Diseases, Xiamen University, Xiamen, Fujian Province, China
| | - An-Mei Deng
- Department of Laboratory Diagnosis, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Liang-Hui Li
- Department of General Surgery, Zhongshan Hospital, Research Institute of Digestive Diseases, Xiamen University, Xiamen, Fujian Province, China
| | - Guo-Yan Liu
- Department of General Surgery, Zhongshan Hospital, Research Institute of Digestive Diseases, Xiamen University, Xiamen, Fujian Province, China
| | - Guo-Yang Wu
- Department of General Surgery, Zhongshan Hospital, Research Institute of Digestive Diseases, Xiamen University, Xiamen, Fujian Province, China
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63
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Liu T, Ren D, Zhu X, Yin Z, Jin G, Zhao Z, Robinson D, Li X, Wong K, Cui K, Zhao H, Wong STC. Transcriptional signaling pathways inversely regulated in Alzheimer's disease and glioblastoma multiform. Sci Rep 2013; 3:3467. [PMID: 24322672 PMCID: PMC4894382 DOI: 10.1038/srep03467] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 11/25/2013] [Indexed: 12/25/2022] Open
Abstract
Convincing epidemiological data suggest an inverse association between cancer and neurodegeneration, including Alzheimer's disease (AD). Since both AD and cancer are characterized by abnormal, but opposing cellular behavior, i.e., increased cell death in AD while excessive cell growth occurs in cancer, this motivates us to initiate the study into unraveling the shared genes and cell signaling pathways linking AD and glioblastoma multiform (GBM). In this study, a comprehensive bioinformatics analysis on clinical microarray datasets of 1,091 GBM and 524 AD cohorts was performed. Significant genes and pathways were identified from the bioinformatics analyses – in particular ERK/MAPK signaling, up-regulated in GBM and Angiopoietin Signaling pathway, reciprocally up-regulated in AD – connecting GBM and AD (P < 0.001), were investigated in details for their roles in GBM growth in an AD environment. Our results showed that suppression of GBM growth in an AD background was mediated by the ERK-AKT-p21-cell cycle pathway and anti-angiogenesis pathway.
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Affiliation(s)
- Timothy Liu
- 1] Department of Systems Medicine and Bioengineering, Houston Methodist Research Institute, Weill Cornell Medical College, Houston, TX 77030 [2]
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Abstract
The PI3K pathway is over-activated in the majority of human cancers. This may occur through oncogenic activation of upstream RAS isoforms and tyrosine kinase receptors, or by mutational activation of components of the PI3K pathway themselves. Stimulation of the PI3K pathway enhances growth, survival, and metabolism of cancer cells. Migration, invasion, and angiogenesis are also supported by PI3K signaling. Thus, the PI3K pathway is an attractive candidate for the therapeutic targeting of tumors. Multiple kinases within the PI3Ks, AKT, and mTOR pathway have been selected for inhibition, and dual inhibitors have also been produced. Recently, the development of kinase inhibitors with enhanced specificity and improved pharmacokinetics has facilitated the investigation of PI3K pathway inhibition in clinical trials. Initial reports are encouraging, with tolerable toxicity profiles reported. PI3K inhibitors have provided some benefit as single-agent treatments of advanced solid tumors and the possibilities for enhanced effect with combination treatments look promising. In this chapter, we describe the PI3K inhibitors currently under investigation for the treatment of cancer and discuss the opportunities and obstacles that have been revealed by the latest preclinical and clinical studies.
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Affiliation(s)
- Clare Sheridan
- Signal Transduction Laboratory, Cancer Research UK London Research Institute, London, United Kingdom.
| | - Julian Downward
- Signal Transduction Laboratory, Cancer Research UK London Research Institute, London, United Kingdom; Lung Cancer Group, Division of Cancer Biology, The Institute of Cancer Research, London, United Kingdom.
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Morris MK, Chi A, Melas IN, Alexopoulos LG. Phosphoproteomics in drug discovery. Drug Discov Today 2013; 19:425-32. [PMID: 24141136 DOI: 10.1016/j.drudis.2013.10.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 09/05/2013] [Accepted: 10/10/2013] [Indexed: 12/20/2022]
Abstract
Several important aspects of the drug discovery process, including target identification, mechanism of action determination and biomarker identification as well as drug repositioning, require complete understanding of the effects of drugs on protein phosphorylation in relevant biological systems. Novel high-throughput phosphoproteomic technologies can be employed to measure these phosphorylation events. In this review, we describe the advantages and limitations of state-of-the-art phosphoproteomic approaches such as mass spectrometry and antibody-based technologies in terms of sample and data throughput as well as data quality. We then discuss how datasets from each technology can be analyzed and how the results can be and have been applied to advance different aspects of the drug discovery process.
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Affiliation(s)
| | - An Chi
- Merck & Co., Boston, MA, USA
| | - Ioannis N Melas
- ProtATonce Ltd, Athens, Greece; Department of Mechanical Engineering, National Technical University of Athens, Athens, Greece
| | - Leonidas G Alexopoulos
- ProtATonce Ltd, Athens, Greece; Department of Mechanical Engineering, National Technical University of Athens, Athens, Greece.
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66
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Zhao H, Jin G, Cui K, Ren D, Liu T, Chen P, Wong S, Li F, Fan Y, Rodriguez A, Chang J, Wong STC. Novel modeling of cancer cell signaling pathways enables systematic drug repositioning for distinct breast cancer metastases. Cancer Res 2013; 73:6149-63. [PMID: 24097821 DOI: 10.1158/0008-5472.can-12-4617] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A new type of signaling network element, called cancer signaling bridges (CSB), has been shown to have the potential for systematic and fast-tracked drug repositioning. On the basis of CSBs, we developed a computational model to derive specific downstream signaling pathways that reveal previously unknown target-disease connections and new mechanisms for specific cancer subtypes. The model enables us to reposition drugs based on available patient gene expression data. We applied this model to repurpose known or shelved drugs for brain, lung, and bone metastases of breast cancer with the hypothesis that cancer subtypes have their own specific signaling mechanisms. To test the hypothesis, we addressed specific CSBs for each metastasis that satisfy (i) CSB proteins are activated by the maximal number of enriched signaling pathways specific to a given metastasis, and (ii) CSB proteins are involved in the most differential expressed coding genes specific to each breast cancer metastasis. The identified signaling networks for the three types of breast cancer metastases contain 31, 15, and 18 proteins and are used to reposition 15, 9, and 2 drug candidates for the brain, lung, and bone metastases. We conducted both in vitro and in vivo preclinical experiments as well as analysis on patient tumor specimens to evaluate the targets and repositioned drugs. Of special note, we found that the Food and Drug Administration-approved drugs, sunitinib and dasatinib, prohibit brain metastases derived from breast cancer, addressing one particularly challenging aspect of this disease.
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Affiliation(s)
- Hong Zhao
- Authors' Affiliations: Department of Systems Medicine and Bioengineering; NCI Center for Modeling Cancer Development, The Methodist Hospital Research Institute, Weill Cornell Medical College; Methodist Cancer Center, The Methodist Hospital; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston; and The University of Texas at Austin, Austin, Texas
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67
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Advanced systems biology methods in drug discovery and translational biomedicine. BIOMED RESEARCH INTERNATIONAL 2013; 2013:742835. [PMID: 24171171 PMCID: PMC3792523 DOI: 10.1155/2013/742835] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 08/26/2013] [Indexed: 02/08/2023]
Abstract
Systems biology is in an exponential development stage in recent years and has been widely utilized in biomedicine to better understand the molecular basis of human disease and the mechanism of drug action. Here, we discuss the fundamental concept of systems biology and its two computational methods that have been commonly used, that is, network analysis and dynamical modeling. The applications of systems biology in elucidating human disease are highlighted, consisting of human disease networks, treatment response prediction, investigation of disease mechanisms, and disease-associated gene prediction. In addition, important advances in drug discovery, to which systems biology makes significant contributions, are discussed, including drug-target networks, prediction of drug-target interactions, investigation of drug adverse effects, drug repositioning, and drug combination prediction. The systems biology methods and applications covered in this review provide a framework for addressing disease mechanism and approaching drug discovery, which will facilitate the translation of research findings into clinical benefits such as novel biomarkers and promising therapies.
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68
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Deyati A, Younesi E, Hofmann-Apitius M, Novac N. Challenges and opportunities for oncology biomarker discovery. Drug Discov Today 2013; 18:614-24. [DOI: 10.1016/j.drudis.2012.12.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 11/28/2012] [Accepted: 12/24/2012] [Indexed: 12/21/2022]
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69
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Lauber MA, Koza SM, McCall SA, Alden BA, Iraneta PC, Fountain KJ. High-Resolution Peptide Mapping Separations with MS-Friendly Mobile Phases and Charge-Surface-Modified C18. Anal Chem 2013; 85:6936-44. [DOI: 10.1021/ac401481z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Matthew A. Lauber
- Waters Corporation, 34 Maple
Street, Milford, Massachusetts 01757-3696, United States
| | - Stephan M. Koza
- Waters Corporation, 34 Maple
Street, Milford, Massachusetts 01757-3696, United States
| | - Scott A. McCall
- Waters Corporation, 34 Maple
Street, Milford, Massachusetts 01757-3696, United States
| | - Bonnie A. Alden
- Waters Corporation, 34 Maple
Street, Milford, Massachusetts 01757-3696, United States
| | - Pamela C. Iraneta
- Waters Corporation, 34 Maple
Street, Milford, Massachusetts 01757-3696, United States
| | - Kenneth J. Fountain
- Waters Corporation, 34 Maple
Street, Milford, Massachusetts 01757-3696, United States
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70
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Tan WH, Popel AS, Mac Gabhann F. Computational Model of Gab1/2-Dependent VEGFR2 Pathway to Akt Activation. PLoS One 2013; 8:e67438. [PMID: 23805312 PMCID: PMC3689841 DOI: 10.1371/journal.pone.0067438] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 05/20/2013] [Indexed: 11/18/2022] Open
Abstract
Vascular endothelial growth factor (VEGF) signal transduction is central to angiogenesis in development and in pathological conditions such as cancer, retinopathy and ischemic diseases. However, no detailed mass-action models of VEGF receptor signaling have been developed. We constructed and validated the first computational model of VEGFR2 trafficking and signaling, to study the opposing roles of Gab1 and Gab2 in regulation of Akt phosphorylation in VEGF-stimulated endothelial cells. Trafficking parameters were optimized against 5 previously published in vitro experiments, and the model was validated against six independent published datasets. The model showed agreement at several key nodes, involving scaffolding proteins Gab1, Gab2 and their complexes with Shp2. VEGFR2 recruitment of Gab1 is greater in magnitude, slower, and more sustained than that of Gab2. As Gab2 binds VEGFR2 complexes more transiently than Gab1, VEGFR2 complexes can recycle and continue to participate in other signaling pathways. Correspondingly, the simulation results show a log-linear relationship between a decrease in Akt phosphorylation and Gab1 knockdown while a linear relationship was observed between an increase in Akt phosphorylation and Gab2 knockdown. Global sensitivity analysis demonstrated the importance of initial-concentration ratios of antagonistic molecular species (Gab1/Gab2 and PI3K/Shp2) in determining Akt phosphorylation profiles. It also showed that kinetic parameters responsible for transient Gab2 binding affect the system at specific nodes. This model can be expanded to study multiple signaling contexts and receptor crosstalk and can form a basis for investigation of therapeutic approaches, such as tyrosine kinase inhibitors (TKIs), overexpression of key signaling proteins or knockdown experiments.
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Affiliation(s)
- Wan Hua Tan
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
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71
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Zhuang G, Yu K, Jiang Z, Chung A, Yao J, Ha C, Toy K, Soriano R, Haley B, Blackwood E, Sampath D, Bais C, Lill JR, Ferrara N. Phosphoproteomic analysis implicates the mTORC2-FoxO1 axis in VEGF signaling and feedback activation of receptor tyrosine kinases. Sci Signal 2013; 6:ra25. [PMID: 23592840 DOI: 10.1126/scisignal.2003572] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The vascular endothelial growth factor (VEGF) signaling pathway plays a pivotal role in normal development and also represents a major therapeutic target for tumors and intraocular neovascular disorders. The VEGF receptor tyrosine kinases promote angiogenesis by phosphorylating downstream proteins in endothelial cells. We applied a large-scale proteomic approach to define the VEGF-regulated phosphoproteome and its temporal dynamics in human umbilical vein endothelial cells and then used siRNA (small interfering RNA) screens to investigate the function of a subset of these phosphorylated proteins in VEGF responses. The PI3K (phosphatidylinositol 3-kinase)-mTORC2 (mammalian target of rapamycin complex 2) axis emerged as central in activating VEGF-regulated phosphorylation and increasing endothelial cell viability by suppressing the activity of the transcription factor FoxO1 (forkhead box protein O1), an effect that limited cellular apoptosis and feedback activation of receptor tyrosine kinases. This FoxO1-mediated feedback loop not only reduced the effectiveness of mTOR inhibitors at decreasing protein phosphorylation and cell survival but also rendered cells more susceptible to PI3K inhibition. Collectively, our study provides a global and dynamic view of VEGF-regulated phosphorylation events and implicates the mTORC2-FoxO1 axis in VEGF receptor signaling and reprogramming of receptor tyrosine kinases in human endothelial cells.
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Affiliation(s)
- Guanglei Zhuang
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
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72
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Wik E, Birkeland E, Trovik J, Werner HM, Hoivik EA, Mjos S, Krakstad C, Kusonmano K, Mauland K, Stefansson IM, Holst F, Petersen K, Oyan AM, Simon R, Kalland KH, Ricketts W, Akslen LA, Salvesen HB. High Phospho-Stathmin(Serine38) Expression Identifies Aggressive Endometrial Cancer and Suggests an Association with PI3K Inhibition. Clin Cancer Res 2013; 19:2331-41. [DOI: 10.1158/1078-0432.ccr-12-3413] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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73
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Goh WWB, Wong L. Networks in proteomics analysis of cancer. Curr Opin Biotechnol 2013; 24:1122-8. [PMID: 23481377 DOI: 10.1016/j.copbio.2013.02.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 01/07/2013] [Accepted: 02/09/2013] [Indexed: 01/08/2023]
Abstract
Proteomics provides direct biological information on proteins but is still a limited platform. Borrowing from genomics, its cancer-specific applications can be broadly categorized as (1) pure diagnostics, (2) biomarkers, (3) identification of root causes and (4) identification of cancer-specific network rewirings. Biological networks capture complex relationships between proteins and provide an appropriate means of contextualization. While playing significantly larger roles, especially in 1 and 3, progress in proteomics-specific network-based methods is lagging as compared to genomics. Rapid hardware advances and improvements in proteomic identification and quantification have given rise to much better quality data alongside advent of new network-based analysis methods. However, a tighter integration between analytics and hardware is still essential for network analysis to play more significant roles in proteomics analysis.
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Affiliation(s)
- Wilson Wen Bin Goh
- Department of Computer Science, National University of Singapore, COM1 Building, 13 Computing Drive, Singapore 117417, Singapore; Department of Computing, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
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74
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Koziol J, Griffin N, Long F, Li Y, Latterich M, Schnitzer J. On protein abundance distributions in complex mixtures. Proteome Sci 2013; 11:5. [PMID: 23360617 PMCID: PMC3599228 DOI: 10.1186/1477-5956-11-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2011] [Accepted: 05/15/2012] [Indexed: 11/20/2022] Open
Abstract
Mass spectrometry, an analytical technique that measures the mass-to-charge ratio of ionized atoms or molecules, dates back more than 100 years, and has both qualitative and quantitative uses for determining chemical and structural information. Quantitative proteomic mass spectrometry on biological samples focuses on identifying the proteins present in the samples, and establishing the relative abundances of those proteins. Such protein inventories create the opportunity to discover novel biomarkers and disease targets. We have previously introduced a normalized, label-free method for quantification of protein abundances under a shotgun proteomics platform (Griffin et al., 2010). The introduction of this method for quantifying and comparing protein levels leads naturally to the issue of modeling protein abundances in individual samples. We here report that protein abundance levels from two recent proteomics experiments conducted by the authors can be adequately represented by Sichel distributions. Mathematically, Sichel distributions are mixtures of Poisson distributions with a rather complex mixing distribution, and have been previously and successfully applied to linguistics and species abundance data. The Sichel model can provide a direct measure of the heterogeneity of protein abundances, and can reveal protein abundance differences that simpler models fail to show.
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Affiliation(s)
- Ja Koziol
- The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, CA, 92037, USA.
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75
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Cell survival and apoptosis signaling as therapeutic target for cancer: marine bioactive compounds. Int J Mol Sci 2013; 14:2334-54. [PMID: 23348928 PMCID: PMC3587990 DOI: 10.3390/ijms14022334] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 01/10/2013] [Accepted: 01/11/2013] [Indexed: 02/06/2023] Open
Abstract
Inhibition of apoptosis leads to activation of cell survival factors (e.g., AKT) causes continuous cell proliferation in cancer. Apoptosis, the major form of cellular suicide, is central to various physiological processes and the maintenance of homeostasis in multicellular organisms. A number of discoveries have clarified the molecular mechanism of apoptosis, thus clarifying the link between apoptosis and cell survival factors, which has a therapeutic outcome. Induction of apoptosis and inhibition of cell survival by anticancer agents has been shown to correlate with tumor response. Cellular damage induces growth arrest and tumor suppression by inducing apoptosis, necrosis and senescence; the mechanism of cell death depends on the magnitude of DNA damage following exposure to various anticancer agents. Apoptosis is mainly regulated by cell survival and proliferating signaling molecules. As a new therapeutic strategy, alternative types of cell death might be exploited to control and eradicate cancer cells. This review discusses the signaling of apoptosis and cell survival, as well as the potential contribution of marine bioactive compounds, suggesting that new therapeutic strategies might follow.
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76
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Abstract
Cells respond to external stimuli by transducing signals through a series of intracellular molecules and eliciting an appropriate response. The cascade of events through which the signals are transduced include post-translational modifications such as phosphorylation and ubiquitylation in addition to formation of multi-protein complexes. Improvements in biological mass spectrometry and protein/peptide microarray technology have tremendously improved our ability to probe proteins, protein complexes, and signaling pathways in a high-throughput fashion. Today, a single mass spectrometry-based investigation of a signaling pathway has the potential to uncover the large majority of known signaling intermediates painstakingly characterized over decades in addition to discovering a number of novel ones. Here, we discuss various proteomic strategies to characterize signaling pathways and provide protocols for phosphoproteomic analysis.
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Affiliation(s)
- H C Harsha
- Institute of Bioinformatics, International Technology Park, Bangalore, India
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77
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Quantitative profiling of DNA damage and apoptotic pathways in UV damaged cells using PTMScan Direct. Int J Mol Sci 2012; 14:286-307. [PMID: 23344034 PMCID: PMC3565264 DOI: 10.3390/ijms14010286] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 12/04/2012] [Accepted: 12/10/2012] [Indexed: 02/07/2023] Open
Abstract
Traditional methods for analysis of peptides using liquid chromatography and tandem mass spectrometry (LC-MS/MS) lack the specificity to comprehensively monitor specific biological processes due to the inherent duty cycle limitations of the MS instrument and the stochastic nature of the analytical platform. PTMScan Direct is a novel, antibody-based method that allows quantitative LC-MS/MS profiling of specific peptides from proteins that reside in the same signaling pathway. New PTMScan Direct reagents have been produced that target peptides from proteins involved in DNA Damage/Cell Cycle and Apoptosis/Autophagy pathways. Together, the reagents provide access to 438 sites on 237 proteins in these signaling cascades. These reagents have been used to profile the response to UV damage of DNA in human cell lines. UV damage was shown to activate canonical DNA damage response pathways through ATM/ATR-dependent signaling, stress response pathways and induce the initiation of apoptosis, as assessed by an increase in the abundance of peptides corresponding to cleaved, activated caspases. These data demonstrate the utility of PTMScan Direct as a multiplexed assay for profiling specific cellular responses to various stimuli, such as UV damage of DNA.
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78
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Pradhan MP, Nagulapalli K, Palakal MJ. Cliques for the identification of gene signatures for colorectal cancer across population. BMC SYSTEMS BIOLOGY 2012; 6 Suppl 3:S17. [PMID: 23282040 PMCID: PMC3524317 DOI: 10.1186/1752-0509-6-s3-s17] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Background Colorectal cancer (CRC) is one of the most commonly diagnosed cancers worldwide. Studies have correlated risk of CRC development with dietary habits and environmental conditions. Gene signatures for any disease can identify the key biological processes, which is especially useful in studying cancer development. Such processes can be used to evaluate potential drug targets. Though recognition of CRC gene-signatures across populations is crucial to better understanding potential novel treatment options for CRC, it remains a challenging task. Results We developed a topological and biological feature-based network approach for identifying the gene signatures across populations. In this work, we propose a novel approach of using cliques to understand the variability within population. Cliques are more conserved and co-expressed, therefore allowing identification and comparison of cliques across a population which can help researchers study gene variations. Our study was based on four publicly available expression datasets belonging to four different populations across the world. We identified cliques of various sizes (0 to 7) across the four population networks. Cliques of size seven were further analyzed across populations for their commonality and uniqueness. Forty-nine common cliques of size seven were identified. These cliques were further analyzed based on their connectivity profiles. We found associations between the cliques and their connectivity profiles across networks. With these clique connectivity profiles (CCPs), we were able to identify the divergence among the populations, important biological processes (cell cycle, signal transduction, and cell differentiation), and related gene pathways. Therefore the genes identified in these cliques and their connectivity profiles can be defined as the gene-signatures across populations. In this work we demonstrate the power and effectiveness of cliques to study CRC across populations. Conclusions We developed a new approach where cliques and their connectivity profiles helped elucidate the variation and similarity in CRC gene profiles across four populations with unique dietary habits.
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Affiliation(s)
- Meeta P Pradhan
- School of Informatics, Indiana University Purdue University Indianapolis, IN, USA
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79
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Altelaar AFM, Munoz J, Heck AJR. Next-generation proteomics: towards an integrative view of proteome dynamics. Nat Rev Genet 2012. [PMID: 23207911 DOI: 10.1038/nrg3356] [Citation(s) in RCA: 515] [Impact Index Per Article: 42.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Next-generation sequencing allows the analysis of genomes, including those representing disease states. However, the causes of most disorders are multifactorial, and systems-level approaches, including the analysis of proteomes, are required for a more comprehensive understanding. The proteome is extremely multifaceted owing to splicing and protein modifications, and this is further amplified by the interconnectivity of proteins into complexes and signalling networks that are highly divergent in time and space. Proteome analysis heavily relies on mass spectrometry (MS). MS-based proteomics is starting to mature and to deliver through a combination of developments in instrumentation, sample preparation and computational analysis. Here we describe this emerging next generation of proteomics and highlight recent applications.
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Affiliation(s)
- A F Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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80
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Iliuk AB, Tao WA. Is phosphoproteomics ready for clinical research? Clin Chim Acta 2012; 420:23-7. [PMID: 23159844 DOI: 10.1016/j.cca.2012.10.063] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 10/31/2012] [Indexed: 12/29/2022]
Abstract
BACKGROUND For many diseases such as cancer where phosphorylation-dependent signaling is the foundation of disease onset and progression, single-gene testing and genomic profiling alone are not sufficient in providing most critical information. The reason for this is that in these activated pathways the signaling changes and drug resistance are often not directly correlated with changes in protein expression levels. In order to obtain the essential information needed to evaluate pathway activation or the effects of certain drugs and therapies on the molecular level, the analysis of changes in protein phosphorylation is critical. METHODS Existing approaches do not differentiate clinical disease subtypes on the protein and signaling pathway level, and therefore hamper the predictive management of the disease and the selection of therapeutic targets. CONCLUSIONS The mini-review examines the impact of emerging systems biology tools and the possibility of applying phosphoproteomics to clinical research.
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Affiliation(s)
- Anton B Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, United States
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Venkateswaran A, Friedman DB, Walsh AJ, Skala MC, Sasi S, Rachakonda G, Crooks PA, Freeman ML, Sekhar KR. The novel antiangiogenic VJ115 inhibits the NADH oxidase ENOX1 and cytoskeleton-remodeling proteins. Invest New Drugs 2012; 31:535-44. [PMID: 23054211 DOI: 10.1007/s10637-012-9884-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 09/24/2012] [Indexed: 01/23/2023]
Abstract
Targeting tumor vasculature represents a rational strategy for controlling cancer. (Z)-(+/-)-2-(1-benzylindol-3-ylmethylene)-1-azabicyclo[2.2.2]octan-3-ol (denoted VJ115) is a novel chemical entity that inhibits the enzyme ENOX1, a NADH oxidase. Genetic and small molecule inhibition of ENOX1 inhibits endothelial cell tubule formation and tumor-mediated neo-angiogenesis. Inhibition of ENOX1 radiosensitizes tumor vasculature, a consequence of enhanced apoptosis. However, the molecular mechanisms underlying these observations are not well understood. Herein, we mechanistically link ENOX1-mediated regulation of cellular NADH concentrations with proteomics profiling of endothelial cell protein expression following exposure to VJ115. Pathway Studios network analysis of potential effector molecules identified by the proteomics profiling indicated that a VJ115 exposure capable of altering intracellular NADH concentrations impacted proteins involved in cytoskeletal reorganization. The analysis was validated using RT-PCR and immunoblotting of selected proteins. RNAi knockdown of ENOX1 was shown to suppress expression of stathmin and lamin A/C, proteins identified by the proteomics analysis to be suppressed upon VJ115 exposure. These data support the hypothesis that VJ115 inhibition of ENOX1 can impact expression of proteins involved in cytoskeletal reorganization and support a hypothesis in which ENOX1 activity links elevated cellular NADH concentrations with cytoskeletal reorganization and angiogenesis.
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82
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Liu S. Epigenetics advancing personalized nanomedicine in cancer therapy. Adv Drug Deliv Rev 2012; 64:1532-43. [PMID: 22921595 DOI: 10.1016/j.addr.2012.08.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 07/27/2012] [Accepted: 08/09/2012] [Indexed: 02/06/2023]
Abstract
Personalized medicine aims to deliver the right drug to a right patient at the right time. It offers unique opportunities to integrate new technologies and concepts to disease prognosis, diagnosis and therapeutics. While selective personalized therapies are conceptually impressive, the majority of cancer therapies have dismal outcome. Such therapeutic failure could result from no response, drug resistance, disease relapse or severe side effect from improper drug delivery. Nanomedicine, the application of nanotechnology in medicine, has a potential to advance the identification of diagnostic and prognostic biomarkers and the delivery of right drug to disease sites. Epigenetic aberrations dynamically contribute to cancer pathogenesis. Given the individualized traits of epigenetic biomarkers, epigenetic considerations would significantly refine personalized nanomedicine. This review aims to dissect the interface of personalized medicine with nanomedicine and epigenetics. I will outline the progress and highlight challenges and areas that can be further explored perfecting the personalized health care.
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D'Andrea S, Berton S, Segatto I, Fabris L, Canzonieri V, Colombatti A, Vecchione A, Belletti B, Baldassarre G. Stathmin is dispensable for tumor onset in mice. PLoS One 2012; 7:e45561. [PMID: 23029098 PMCID: PMC3447788 DOI: 10.1371/journal.pone.0045561] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 08/20/2012] [Indexed: 11/18/2022] Open
Abstract
The microtubule-destabilizing protein stathmin is highly expressed in several types of tumor, thus deserving the name of oncoprotein 18. High levels of stathmin expression and/or activity favor the metastatic spreading and mark the most aggressive tumors, thus representing a realistic marker of poor prognosis. Stathmin is a downstream target of many signaling pathways, including Ras-MAPK, PI3K and p53, involved in both tumor onset and progression. We thus hypothesized that stathmin could also play a role during the early stages of tumorigenesis, an issue completely unexplored. In order to establish whether stathmin expression is necessary for tumor initiation, we challenged wild type (WT), stathmin heterozygous and stathmin knock-out (KO) mice with different carcinogens. Using well-defined mouse models of carcinogenesis of skin, bladder and muscle by the means of 7,12-dimethylbenz[α]antracene (DMBA)/12-O-tetradecanoylphorbol-13-acetate (TPA), N-butyl-N-(4-hydroxybutyl) nitrosamine (BBN) and 3-methylcholanthrylene (3MC) treatments, respectively, we demonstrated that knock-out of stathmin has no impact on the onset of cancer in mice. No significant difference was noticed either when the Ras oncogene was mutated (skin carcinogenesis model) or when the p53 pathway was inactivated (bladder carcinomas and fibrosarcomas). Finally, we concomitantly impinged on p53 and Ras pathways, by generating WT and stathmin KO mouse embryo fibroblasts transformed with papilloma virus large T antigen (LgTAg) plus the K-RasG12V oncogene. In vivo growth of xenografts from these transformed fibroblasts did not highlight any significant difference depending on the presence or absence of stathmin. Overall, our work demonstrates that stathmin expression is dispensable for tumor onset, at least in mice, thus making stathmin a virtually exclusive marker of aggressive disease and a promising therapeutic target for advanced cancers.
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Affiliation(s)
- Sara D'Andrea
- Division of Experimental Oncology 2, CRO, National Cancer Institute, Aviano, Italy
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84
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Younes A, Berry DA. From drug discovery to biomarker-driven clinical trials in lymphoma. Nat Rev Clin Oncol 2012; 9:643-53. [PMID: 22965151 DOI: 10.1038/nrclinonc.2012.156] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Over the past three decades, the pathological classification of lymphoma has substantially improved. The early Rappaport classification included a handful of subtypes that did not reflect the cell of origin and, not surprisingly, resulted in diagnostic inaccuracies. The WHO currently classifies lymphoma into 30 major distinctive types. While this classification improved the accuracy and consistency of the histological diagnosis of lymphoma, it had little impact on advancing drug development or improving the cure rate of this disease. One reason for this lack of improvement is that recent developments in cancer genomics show these histopathological subtypes to be heterogeneous. Basing treatment decisions on histopathological subtypes is inefficient as it groups different underlying molecular characteristics into one category. Such a strategy exposes many patients to potentially toxic drugs without providing benefits. The recent approval of two new cancer drugs with companion diagnostics to allow selection and treatment of patients with melanoma and non-small-cell lung cancer has raised hope that a similar approach may also expedite successful drug development in lymphoma. We review the current status of biomarker development in lymphoma, and discuss novel biomarker-directed clinical trial designs for lymphoma.
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Affiliation(s)
- Anas Younes
- Department of Lymphoma/Myeloma, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.
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85
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Imami K, Sugiyama N, Imamura H, Wakabayashi M, Tomita M, Taniguchi M, Ueno T, Toi M, Ishihama Y. Temporal profiling of lapatinib-suppressed phosphorylation signals in EGFR/HER2 pathways. Mol Cell Proteomics 2012; 11:1741-57. [PMID: 22964224 DOI: 10.1074/mcp.m112.019919] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Lapatinib is a clinically potent kinase inhibitor for breast cancer patients because of its outstanding selectivity for epidermal growth factor receptor (EGFR) and EGFR2 (also known as HER2). However, there is only limited information about the in vivo effects of lapatinib on EGFR/HER2 and downstream signaling targets. Here, we profiled the lapatinib-induced time- and dose-dependent phosphorylation dynamics in SKBR3 breast cancer cells by means of quantitative phosphoproteomics. Among 4953 identified phosphopeptides from 1548 proteins, a small proportion (5-7%) was regulated at least twofold by 1-10 μm lapatinib. We obtained a comprehensive phosphorylation map of 21 sites on EGFR/HER2, including nine novel sites on HER2. Among them, serine/threonine phosphosites located in a small region of HER2 (amino acid residues 1049-1083) were up-regulated by the drug, whereas all other sites were down-regulated. We show that cAMP-dependent protein kinase is involved in phosphorylation of this particular region of HER2 and regulates HER2 tyrosine kinase activity. Computational analyses of quantitative phosphoproteome data indicated for the first time that protein-protein networks related to cytoskeletal organization and transcriptional/translational regulation, such as RNP complexes (i.e. hnRNP, snRNP, telomerase, ribosome), are linked to EGFR/HER2 signaling networks. To our knowledge, this is the first report to profile the temporal response of phosphorylation dynamics to a kinase inhibitor. The results provide new insights into EGFR/HER2 regulation through region-specific phosphorylation, as well as a global view of the cellular signaling networks associated with the anti-breast cancer action of lapatinib.
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Affiliation(s)
- Koshi Imami
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
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86
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Abstract
The B-cell receptor (BCR) complex and its associated protein tyrosine kinases play a critical role in the development, proliferation, and survival of normal or malignant B cells. Regulated activity of the BCR complex promotes the expansion of selected B cells and the deletion of unwanted or self-reactive ones. Compounds that inhibit various components of this pathway, including spleen tyrosine kinase, Bruton's tyrosine kinase, and phosphoinositol-3 kinase, have been developed. We summarize the rationale for use of agents that can inhibit BCR signaling to treat patients with either indolent or aggressive B-cell lymphomas, highlight early clinical results, and speculate on the future application of such agents in the treatment of patients with various B-cell lymphomas.
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MESH Headings
- Adenine/analogs & derivatives
- Aminopyridines
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Lymphoma, Large B-Cell, Diffuse/drug therapy
- Lymphoma, Large B-Cell, Diffuse/metabolism
- Lymphoma, Large B-Cell, Diffuse/pathology
- Lymphoma, Mantle-Cell/drug therapy
- Lymphoma, Mantle-Cell/metabolism
- Lymphoma, Mantle-Cell/pathology
- Morpholines
- Neoplasm Staging
- Niacinamide/analogs & derivatives
- Niacinamide/therapeutic use
- Oxazines/therapeutic use
- Phenylurea Compounds/therapeutic use
- Phosphatidylinositol 3-Kinases/metabolism
- Phosphoinositide-3 Kinase Inhibitors
- Piperidines
- Protein-Tyrosine Kinases/antagonists & inhibitors
- Protein-Tyrosine Kinases/metabolism
- Purines/therapeutic use
- Pyrazoles/therapeutic use
- Pyridines/therapeutic use
- Pyrimidines/therapeutic use
- Quinazolinones/therapeutic use
- Receptors, Antigen, B-Cell/antagonists & inhibitors
- Receptors, Antigen, B-Cell/chemistry
- Receptors, Antigen, B-Cell/metabolism
- Signal Transduction
- Sorafenib
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Affiliation(s)
- Michael Y Choi
- UC San Diego Moores Cancer Center, La Jolla, CA 92093, USA
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87
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Abstract
The PI3K (phosphatidylinositol 3-kinase)-AKT pathway is one of the most important signaling networks in cancer. There is growing evidence that activation of this pathway plays a significant role in melanoma, frequently in the setting of concurrent activation of RAS-RAF-MEK-ERK signaling. This evidence includes the identification of genetic and epigenetic events that activate this pathway in melanoma cell lines and clinical specimens. In addition, functional experiments have demonstrated important roles for the PI3K-AKT pathway in both melanoma initiation and therapeutic resistance. The availability of many inhibitors against the PI3K-AKT pathway is rapidly leading to the development of trials that will ultimately determine its clinical significance in this disease. The rational development of such therapies will be facilitated by strategies that utilize the growing understanding of the complexity of the regulation and roles of this pathway.
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88
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High mass accuracy phosphopeptide identification using tandem mass spectra. INTERNATIONAL JOURNAL OF PROTEOMICS 2012; 2012:104681. [PMID: 22844594 PMCID: PMC3403174 DOI: 10.1155/2012/104681] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 06/18/2012] [Indexed: 12/21/2022]
Abstract
Phosphoproteomics is a powerful analytical platform for identification and quantification of phosphorylated peptides and assignment of phosphorylation sites. Bioinformatics tools to identify phosphorylated peptides from their tandem mass spectra and protein sequence databases are important part of phosphoproteomics. In this work, we discuss general informatics aspects of mass-spectrometry-based phosphoproteomics. Some of the specifics of phosphopeptide identifications stem from the labile nature of phosphor groups and expanded peptide search space. Allowing for modifications of Ser, Thr, and Tyr residues exponentially increases effective database size. High mass resolution and accuracy measurements of precursor mass-to-charge ratios help to restrict the search space of candidate peptide sequences. The higher-order fragmentations of neutral loss ions enhance the fragment ion mass spectra of phosphorylated peptides. We show an example of a phosphopeptide identification where accounting for fragmentation from neutral loss species improves the identification scores in a database search algorithm by 50%.
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89
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Emerging technologies for improved stratification of cancer patients: a review of opportunities, challenges, and tools. Cancer J 2012; 17:451-64. [PMID: 22157289 DOI: 10.1097/ppo.0b013e31823bd1f8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cancer is a heterogeneous collection of diseases with wild variation in etiology, pathogenesis, response to therapy, and prognosis. Sources of variation are frequently obscure. Current practice attempts to classify tumors by tissue of origin and extent of disease through staging such that more risky tumors can be managed with more aggressive treatments. Modest inroads have been made with biomarkers to further characterize groups of tumors with important characteristics such as response to selected drugs. However, biomarker-driven decisions are relatively few when examining the maze of clinical decisions in the care of cancer patients. Against this backdrop, waves of researchers have unleashed a vast array of new technologies, with the goal of better characterization of the inherent diversity of tumors. This review outlines the use of cancer biomarkers and emerging technologies to stratify patients with a focus on the challenges and opportunities of next-generation nucleic acid sequencing approaches in oncology.
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90
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Li X, Rao V, Jin J, Guan B, Anderes KL, Bieberich CJ. Identification and validation of inhibitor-responsive kinase substrates using a new paradigm to measure kinase-specific protein phosphorylation index. J Proteome Res 2012; 11:3637-49. [PMID: 22663298 DOI: 10.1021/pr3000514] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Regulation of all cellular processes requires dynamic regulation of protein phosphorylation. We have developed an unbiased system to globally quantify the phosphorylation index for substrates of a specific kinase by independently quantifying phosphorylated and total substrate molecules in a reverse in-gel kinase assay. Non-phosphorylated substrate molecules are first quantified in the presence and absence of a specific stimulus. Total substrate molecules are then measured after complete chemical dephosphorylation, and a ratio of phosphorylated to total substrate is derived. To demonstrate the utility of this approach, we profiled and quantified changes in phosphorylation index for Protein Kinase CK2 substrates that respond to a small-molecule inhibitor. A broad range of inhibitor-induced changes in phosphorylation was observed in cultured cells. Differences among substrates in the kinetics of phosphorylation change were also revealed. Comparison of CK2 inhibitor-induced changes in phosphorylation in cultured cells and in mouse peripheral blood lymphocytes in vivo revealed distinct kinetic and depth-of-response profiles. This technology provides a new approach to facilitate functional analyses of kinase-specific phosphorylation events. This strategy can be used to dissect the role of phosphorylation in cellular events, to facilitate kinase inhibitor target validation studies, and to inform in vivo analyses of kinase inhibitor drug efficacy.
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Affiliation(s)
- Xiang Li
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
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91
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Wiza C, Nascimento EBM, Ouwens DM. Role of PRAS40 in Akt and mTOR signaling in health and disease. Am J Physiol Endocrinol Metab 2012; 302:E1453-60. [PMID: 22354785 DOI: 10.1152/ajpendo.00660.2011] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The proline-rich Akt substrate of 40 kDa (PRAS40) acts at the intersection of the Akt- and mammalian target of rapamycin (mTOR)-mediated signaling pathways. The protein kinase mTOR is the catalytic subunit of two distinct signaling complexes, mTOR complex 1 (mTORC1) and mTORC2, that link energy and nutrients to the regulation of cellular growth and energy metabolism. Activation of mTOR in response to nutrients and growth factors results in the phosphorylation of numerous substrates, including the phosphorylations of S6 kinase by mTORC1 and Akt by mTORC2. Alterations in Akt and mTOR activity have been linked to the progression of multiple diseases such as cancer and type 2 diabetes. Although PRAS40 was first reported as substrate for Akt, investigations toward mTOR-binding partners subsequently identified PRAS40 as both component and substrate of mTORC1. Phosphorylation of PRAS40 by Akt and by mTORC1 itself results in dissociation of PRAS40 from mTORC1 and may relieve an inhibitory constraint on mTORC1 activity. Adding to the complexity is that gene silencing studies indicate that PRAS40 is also necessary for the activity of the mTORC1 complex. This review summarizes the regulation and potential function(s) of PRAS40 in the complex Akt- and mTOR-signaling network in health and disease.
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Affiliation(s)
- Claudia Wiza
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Düsseldorf, Germany
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92
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Huang JM, Nagatomo I, Suzuki E, Mizuno T, Kumagai T, Berezov A, Zhang H, Karlan B, Greene MI, Wang Q. YAP modifies cancer cell sensitivity to EGFR and survivin inhibitors and is negatively regulated by the non-receptor type protein tyrosine phosphatase 14. Oncogene 2012; 32:2220-9. [PMID: 22689061 PMCID: PMC3443515 DOI: 10.1038/onc.2012.231] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The Yes-associated protein (YAP) is a transcriptional factor involved in tissue development and tumorigenesis. Although YAP has been recognized as a key element of the Hippo signaling pathway, the mechanisms that regulate YAP activities remain to be fully characterized. In this study, we demonstrate that the non-receptor type protein tyrosine phosphatase 14 (PTPN14) functions as a negative regulator of YAP. We show that YAP forms a protein complex with PTPN14 through the WW domains of YAP and the PPXY motifs of PTPN14. In addition, PTPN14 inhibits YAP-mediated transcriptional activities. Knockdown of YAP sensitizes cancer cells to various anti-cancer agents, such as cisplatin, the EGFR tyrosine kinase inhibitor erlotinib, and the small-molecule antagonist of survivin, S12. YAP-targeted modalities may be used in combination with other cancer drugs to achieve maximal therapeutic effects.
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Affiliation(s)
- J-M Huang
- Cedars-Sinai Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute Los Angeles, CA 90048, USA
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93
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Zieba A, Grannas K, Söderberg O, Gullberg M, Nilsson M, Landegren U. Molecular tools for companion diagnostics. N Biotechnol 2012; 29:634-40. [PMID: 22634023 DOI: 10.1016/j.nbt.2012.05.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Revised: 05/11/2012] [Accepted: 05/16/2012] [Indexed: 02/02/2023]
Abstract
The heterogeneous nature of cancer results in highly variable therapeutic responses even among patients with identical stages and grades of a malignancy. The move towards personalised medicine in cancer therapy has therefore been motivated by a need to customise therapy according to molecular features of individual tumours. Companion diagnostics serves to support early drug development, it can provide surrogate markers in clinical trials, and also guide selection of individual therapies and monitoring of responses in routine clinical care. The era of companion diagnostics can be said to have begun with the introduction of the HercepTest - a first-of-a-kind diagnostic tool developed by DakoCytomation in 1998 to select patients for therapy with the anticancer drug Herceptin (trastuzumab). Herceptin and the paired test proved that companion diagnostics can help guide patient-tailored therapies. We will discuss herein technologies to analyse companion diagnostics markers at the level of DNA, RNA or protein, focusing on a series of methods developed in our laboratory that can facilitate drug development and help stratify patients for therapy.
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Affiliation(s)
- Agata Zieba
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, SE-75185 Uppsala, Sweden.
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94
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Klammer M, Kaminski M, Zedler A, Oppermann F, Blencke S, Marx S, Müller S, Tebbe A, Godl K, Schaab C. Phosphosignature predicts dasatinib response in non-small cell lung cancer. Mol Cell Proteomics 2012; 11:651-68. [PMID: 22617229 DOI: 10.1074/mcp.m111.016410] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Targeted drugs are less toxic than traditional chemotherapeutic therapies; however, the proportion of patients that benefit from these drugs is often smaller. A marker that confidently predicts patient response to a specific therapy would allow an individual therapy selection most likely to benefit the patient. Here, we used quantitative mass spectrometry to globally profile the basal phosphoproteome of a panel of non-small cell lung cancer cell lines. The effect of the kinase inhibitor dasatinib on cellular growth was tested against the same panel. From the phosphoproteome profiles, we identified 58 phosphorylation sites, which consistently differ between sensitive and resistant cell lines. Many of the corresponding proteins are involved in cell adhesion and cytoskeleton organization. We showed that a signature of only 12 phosphorylation sites is sufficient to accurately predict dasatinib sensitivity. Four of the phosphorylation sites belong to integrin β4, a protein that mediates cell-matrix or cell-cell adhesion. The signature was validated in cross-validation and label switch experiments and in six independently profiled breast cancer cell lines. The study supports that the phosphorylation of integrin β4, as well as eight further proteins comprising the signature, are candidate biomarkers for predicting response to dasatinib in solid tumors. Furthermore, our results show that identifying predictive phosphorylation signatures from global, quantitative phosphoproteomic data is possible and can open a new path to discovering molecular markers for response prediction.
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95
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Role of phosphatidylinositol-3-kinase pathway in head and neck squamous cell carcinoma. JOURNAL OF ONCOLOGY 2012; 2012:450179. [PMID: 22666248 PMCID: PMC3362130 DOI: 10.1155/2012/450179] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Accepted: 03/14/2012] [Indexed: 01/04/2023]
Abstract
Activation of the phosphatidylinositol-3-kinase (PI3K) pathway is one of the most frequently observed molecular alterations in many human malignancies, including head and neck squamous cell carcinoma (HNSCC). A growing body of evidence demonstrates the prime importance of the PI3K pathway at each stage of tumorigenesis, that is, tumor initiation, progression, recurrence, and metastasis. Expectedly, targeting the PI3K pathway yields some promising results in both preclinical studies and clinical trials for certain cancer patients. However, there are still many questions that need to be answered, given the complexity of this pathway and the existence of its multiple feedback loops and interactions with other signaling pathways. In this paper, we will summarize recent advances in the understanding of the PI3K pathway role in human malignancies, with an emphasis on HNSCC, and discuss the clinical applications and future direction of this field.
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96
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Abstract
A defining feature of many cancers is deregulated translational control. Typically, this occurs at the level of recruitment of the 40S ribosomes to the 5'-cap of cellular messenger RNAs (mRNAs), the rate-limiting step of protein synthesis, which is controlled by the heterotrimeric eukaryotic initiation complex eIF4F. Thus, eIF4F in particular, and translation initiation in general, represent an exploitable vulnerability and unique opportunity for therapeutic intervention in many transformed cells. In this article, we discuss the development, mode of action and biological activity of a number of small-molecule inhibitors that interrupt PI3K/mTOR signaling control of eIF4F assembly, as well as compounds that more directly block eIF4F activity.
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Affiliation(s)
- Abba Malina
- Department of Biochemistry and McGill University, Montréal, Québec H3G 1Y6, Canada
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97
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Hanash S, Schliekelman M, Zhang Q, Taguchi A. Integration of proteomics into systems biology of cancer. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2012; 4:327-37. [PMID: 22407608 DOI: 10.1002/wsbm.1169] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Deciphering the complexity and heterogeneity of cancer, benefits from integration of proteomic level data into systems biology efforts. The opportunities available as a result of advances in proteomic technologies, the successes to date, and the challenges involved in integrating diverse datasets are addressed in this review.
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Affiliation(s)
- S Hanash
- Molecular Diagnostics Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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98
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Kim J, Otto N, Conti CJ, Gimenz-Conti IB, Walker CL. Immunohistochemical analysis of mTOR activity in tissues. Methods Mol Biol 2012; 821:215-225. [PMID: 22125067 DOI: 10.1007/978-1-61779-430-8_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
mTOR is a key regulator of cell growth and size, and its activity is often dysregulated in a wide variety of diseases. The mTOR signaling pathway is also a therapeutic target for many diseases, including cancer. Immunohistochemistry is a powerful method to assess mTOR activity in clinical/histological samples, however, care should be taken in choosing the targets for determining mTOR activity due to the complexity of its regulation. This chapter describes the most up-to-date methods for visualizing mTOR activity by immunohistochemistry using commercially available antibodies, including considerations for validating new antibodies for assessing mTOR signaling.
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Affiliation(s)
- Jinhee Kim
- Department of Molecular Carcinogenesis, The University of Texas M. D. Anderson Cancer Center, Smithville, TX, USA
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99
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Boschetti E, Chung MCM, Righetti PG. "The quest for biomarkers": are we on the right technical track? Proteomics Clin Appl 2011; 6:22-41. [PMID: 22213582 DOI: 10.1002/prca.201100039] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 10/01/2011] [Accepted: 11/15/2011] [Indexed: 12/19/2022]
Abstract
The discovery phase of biomarkers of diagnostic or therapeutic interest started a decade ago with the very rapid development of proteomic investigations. In spite of the development of innovative technologies and multiple approaches, the "harvest" is still modest. Various reasons justified the encountered difficulties and most of them have been circumvented by specific sample treatments or dedicated analytical approaches. Nevertheless, the situation of very modest biomarker discovery level did not change much. This review intends to specifically analyze the main approaches used for biomarker discovery phase and evaluate related advantages and disadvantages. Thus, preliminary sample treatments such as fractionation, depletion and reduction of dynamic concentration range will critically be discussed and then the main differential expression investigation methods analyzed. Combinations of technologies are also discussed along with possible proposals to federate associations of complementary technologies for better chances of success.
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Affiliation(s)
- Egisto Boschetti
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milano, Italy.
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100
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Adamo B, Deal AM, Burrows E, Geradts J, Hamilton E, Blackwell KL, Livasy C, Fritchie K, Prat A, Harrell JC, Ewend MG, Carey LA, Miller CR, Anders CK. Phosphatidylinositol 3-kinase pathway activation in breast cancer brain metastases. Breast Cancer Res 2011; 13:R125. [PMID: 22132754 PMCID: PMC3326567 DOI: 10.1186/bcr3071] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 09/27/2011] [Accepted: 12/01/2011] [Indexed: 11/30/2022] Open
Abstract
INTRODUCTION Activation status of the phosphatidylinositol 3-kinase (PI3K) pathway in breast cancer brain metastases (BCBMs) is largely unknown. We examined expression of phospho(p)-AKT, p-S6, and phosphatase and tensin homologue (PTEN) in BCBMs and their implications for overall survival (OS) and survival after BCBMs. Secondary analyses included PI3K pathway activation status and associations with time to distant recurrence (TTDR) and time to BCBMs. Similar analyses were also conducted among the subset of patients with triple-negative BCBMs. METHODS p-AKT, p-S6, and PTEN expression was assessed with immunohistochemistry in 52 BCBMs and 12 matched primary BCs. Subtypes were defined as hormone receptor (HR)+/HER2-, HER2+, and triple-negative (TNBC). Survival analyses were performed by using a Cox model, and survival curves were estimated with the Kaplan-Meier method. RESULTS Expression of p-AKT and p-S6 and lack of PTEN (PTEN-) was observed in 75%, 69%, and 25% of BCBMs. Concordance between primary BCs and matched BCBMs was 67% for p-AKT, 58% for p-S6, and 83% for PTEN. PTEN- was more common in TNBC compared with HR+/HER2- and HER2+. Expression of p-AKT, p-S6, and PTEN- was not associated with OS or survival after BCBMs (all, P > 0.06). Interestingly, among all patients, PTEN- correlated with shorter time to distant and brain recurrence. Among patients with TNBC, PTEN- in BCBMs was associated with poorer overall survival. CONCLUSIONS The PI3K pathway is active in most BCBMs regardless of subtype. Inhibition of this pathway represents a promising therapeutic strategy for patients with BCBMs, a group of patients with poor prognosis and limited systemic therapeutic options. Although expression of the PI3K pathway did not correlate with OS and survival after BCBM, PTEN- association with time to recurrence and OS (among patients with TNBC) is worthy of further study.
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Affiliation(s)
- Barbara Adamo
- Department of Medicine, Division of Hematology-Oncology, CB 7305, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Human Pathology, Integrated Therapies in Oncology Unit, University of Messina, Messina 98125, Italy
- Lineberger Comprehensive Cancer Center, 170 Manning Drive, CB 7350, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Allison M Deal
- Department of Biostatistics and Clinical Data Management, Lineberger Comprehensive Cancer Center, Manning Drive, CB 7350, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Emily Burrows
- Lineberger Comprehensive Cancer Center, 170 Manning Drive, CB 7350, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Joseph Geradts
- Department of Pathology, Duke University Medical Center, Box 3712, Durham, NC 27710, USA
| | - Erika Hamilton
- Department of Medicine, Division of Hematology-Oncology, 382 Hanes Building, Duke University Medical Center, Box 102382, Durham, NC 27710, USA
| | - Kimberly L Blackwell
- Department of Medicine, Division of Hematology-Oncology, 382 Hanes Building, Duke University Medical Center, Box 102382, Durham, NC 27710, USA
| | - Chad Livasy
- Department of Pathology, Carolinas Medical Center, P.O. Box 32187, Charlotte, NC 28232, USA
| | - Karen Fritchie
- Department of Pathology, Mayo Clinic, 13400 East Shea Boulevard, Rochester, MN 85259, USA
| | - Aleix Prat
- Lineberger Comprehensive Cancer Center, 170 Manning Drive, CB 7350, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Genetics, 120 Mason Farm Road, CB#7264, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Pathology & Laboratory Medicine, CB#7525, University of North Carolina, Chapel Hill, NC 27599, USA
| | - J Chuck Harrell
- Lineberger Comprehensive Cancer Center, 170 Manning Drive, CB 7350, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Genetics, 120 Mason Farm Road, CB#7264, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Pathology & Laboratory Medicine, CB#7525, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Matthew G Ewend
- Lineberger Comprehensive Cancer Center, 170 Manning Drive, CB 7350, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Neurosurgery, CB 7250, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Lisa A Carey
- Department of Medicine, Division of Hematology-Oncology, CB 7305, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, 170 Manning Drive, CB 7350, University of North Carolina, Chapel Hill, NC 27599, USA
| | - C Ryan Miller
- Lineberger Comprehensive Cancer Center, 170 Manning Drive, CB 7350, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Pathology & Laboratory Medicine, CB#7525, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Carey K Anders
- Department of Medicine, Division of Hematology-Oncology, CB 7305, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, 170 Manning Drive, CB 7350, University of North Carolina, Chapel Hill, NC 27599, USA
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