251
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Wiśniewski JR. Label-Free and Standard-Free Absolute Quantitative Proteomics Using the "Total Protein" and "Proteomic Ruler" Approaches. Methods Enzymol 2016; 585:49-60. [PMID: 28109442 DOI: 10.1016/bs.mie.2016.10.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Understanding biological systems and their variation upon stimuli requires knowledge on their composition, primarily including information on organization and dynamics of proteomes. The total protein approach (TPA) is a label- and standard-free method for absolute protein quantitation of proteins using large-scale proteomic data. The method relies on the assumption that the total MS signal from all identified proteins in the dataset reflects-in a biochemical sense-the total protein and the MS signal from a single protein corresponds its abundance in the studied sample. The method offers an easy way to quantify thousands of protein per sample. A related method, the "Proteomic Ruler," enables conversion of the protein abundance data calculated by TPA to compute numbers of protein copies per cell. TPA and the Proteomic Ruler are powerful tools for studying dynamics of cell architecture.
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Affiliation(s)
- J R Wiśniewski
- Biochemical Proteomics Group, Max-Planck-Institute of Biochemistry, Martinsried, Germany.
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252
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Nakpheng T, Songkarak S, Suwandecha T, Sritharadol R, Chunhachaichana C, Srichana T. Evidences for salbutamol metabolism by respiratory and liver cell lines. Drug Metab Pharmacokinet 2016; 32:127-134. [PMID: 28318879 DOI: 10.1016/j.dmpk.2016.11.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Revised: 08/31/2016] [Accepted: 11/10/2016] [Indexed: 01/13/2023]
Abstract
This study aimed to investigate the enantiomeric biotransformation of salbutamol in the human respiratory and liver cells. The cells from the different cell growth cycles were treated with various concentrations of salbutamol sulfate. Salbutamol and its metabolites were analyzed using chiral liquid chromatography and mass spectrometry. There were no metabolites of salbutamol found in the extracellular medium, intracellular, and cell lysate of respiratory cell lines. The S/R ratios of salbutamol were found to be 0.99-1.10 in all cell lines, cell cycles, and salbutamol concentrations in this study. Salbutamol metabolites were found only in intracellular HepG2 cells. The S/R ratios of the salbutamol inside the liver cells were 10 times greater than the S/R ratios of the salbutamol in the liver extracellular medium (0.99-1.10). It is important to note that the S/R ratios of salbutamol in liver cell lysate enzyme were 0.99-1.10 whereas the S/R salbutamol metabolites inside the liver cell were around 1.91-2.14. Both salbutamol and sulfate conjugation metabolites were detected in MS chromatograms with an m/z of 239.2 and 317.6, respectively. Hence, the delivery of salbutamol directly to the respiratory system is a right target that can avoid first-pass metabolism.
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Affiliation(s)
- Titpawan Nakpheng
- Drug Delivery System Excellence Center and Nanotec-PSU Excellence Center in Drug Delivery, Prince of Songkla University, Hat-Yai, Songkhla, 90112, Thailand
| | - Supreedee Songkarak
- Department of the Pharmaceutical Technology, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Hat-Yai, Songkhla, 90112, Thailand
| | - Tan Suwandecha
- Drug Delivery System Excellence Center and Nanotec-PSU Excellence Center in Drug Delivery, Prince of Songkla University, Hat-Yai, Songkhla, 90112, Thailand; Department of Pharmacology, Faculty of Sciences, Prince of Songkla University, Hat-Yai, Songkhla, 90112, Thailand
| | - Rutthapol Sritharadol
- Drug Delivery System Excellence Center and Nanotec-PSU Excellence Center in Drug Delivery, Prince of Songkla University, Hat-Yai, Songkhla, 90112, Thailand; Department of the Pharmaceutical Technology, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Hat-Yai, Songkhla, 90112, Thailand
| | - Charisopon Chunhachaichana
- Drug Delivery System Excellence Center and Nanotec-PSU Excellence Center in Drug Delivery, Prince of Songkla University, Hat-Yai, Songkhla, 90112, Thailand; Department of the Pharmaceutical Technology, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Hat-Yai, Songkhla, 90112, Thailand
| | - Teerapol Srichana
- Drug Delivery System Excellence Center and Nanotec-PSU Excellence Center in Drug Delivery, Prince of Songkla University, Hat-Yai, Songkhla, 90112, Thailand; Department of the Pharmaceutical Technology, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Hat-Yai, Songkhla, 90112, Thailand.
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253
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Neul C, Schaeffeler E, Sparreboom A, Laufer S, Schwab M, Nies AT. Impact of Membrane Drug Transporters on Resistance to Small-Molecule Tyrosine Kinase Inhibitors. Trends Pharmacol Sci 2016; 37:904-932. [PMID: 27659854 DOI: 10.1016/j.tips.2016.08.003] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 08/18/2016] [Accepted: 08/19/2016] [Indexed: 12/21/2022]
Abstract
Small-molecule inhibitors of tyrosine kinases (TKIs) are the mainstay of treatment for many malignancies and represent novel treatment options for other diseases such as idiopathic pulmonary fibrosis. Twenty-five TKIs are currently FDA-approved and >130 are being evaluated in clinical trials. Increasing evidence suggests that drug exposure of TKIs may significantly contribute to drug resistance, independently from somatic variation of TKI target genes. Membrane transport proteins may limit the amount of TKI reaching the target cells. This review highlights current knowledge on the basic and clinical pharmacology of membrane transporters involved in TKI disposition and their contribution to drug efficacy and adverse drug effects. In addition to non-genetic and epigenetic factors, genetic variants, particularly rare ones, in transporter genes are promising novel factors to explain interindividual variability in the response to TKI therapy.
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Affiliation(s)
- Claudia Neul
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, and University of Tübingen, Germany
| | - Elke Schaeffeler
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, and University of Tübingen, Germany
| | - Alex Sparreboom
- Division of Pharmaceutics, College of Pharmacy, Ohio State University, Columbus, OH, USA
| | - Stefan Laufer
- Department of Pharmaceutical Chemistry, University of Tübingen, Tübingen, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, and University of Tübingen, Germany; Department of Clinical Pharmacology, Institute of Experimental and Clinical Pharmacology and Toxicology, University Hospital, Tübingen, Germany; Department of Pharmacy and Biochemistry, University of Tübingen, Tübingen, Germany.
| | - Anne T Nies
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, and University of Tübingen, Germany
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254
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Subcellular fractionation of human liver reveals limits in global proteomic quantification from isolated fractions. Anal Biochem 2016; 509:82-88. [DOI: 10.1016/j.ab.2016.06.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 06/04/2016] [Indexed: 11/19/2022]
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255
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Merkle R, Steiert B, Salopiata F, Depner S, Raue A, Iwamoto N, Schelker M, Hass H, Wäsch M, Böhm ME, Mücke O, Lipka DB, Plass C, Lehmann WD, Kreutz C, Timmer J, Schilling M, Klingmüller U. Identification of Cell Type-Specific Differences in Erythropoietin Receptor Signaling in Primary Erythroid and Lung Cancer Cells. PLoS Comput Biol 2016; 12:e1005049. [PMID: 27494133 PMCID: PMC4975441 DOI: 10.1371/journal.pcbi.1005049] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 07/05/2016] [Indexed: 01/23/2023] Open
Abstract
Lung cancer, with its most prevalent form non-small-cell lung carcinoma (NSCLC), is one of the leading causes of cancer-related deaths worldwide, and is commonly treated with chemotherapeutic drugs such as cisplatin. Lung cancer patients frequently suffer from chemotherapy-induced anemia, which can be treated with erythropoietin (EPO). However, studies have indicated that EPO not only promotes erythropoiesis in hematopoietic cells, but may also enhance survival of NSCLC cells. Here, we verified that the NSCLC cell line H838 expresses functional erythropoietin receptors (EPOR) and that treatment with EPO reduces cisplatin-induced apoptosis. To pinpoint differences in EPO-induced survival signaling in erythroid progenitor cells (CFU-E, colony forming unit-erythroid) and H838 cells, we combined mathematical modeling with a method for feature selection, the L1 regularization. Utilizing an example model and simulated data, we demonstrated that this approach enables the accurate identification and quantification of cell type-specific parameters. We applied our strategy to quantitative time-resolved data of EPO-induced JAK/STAT signaling generated by quantitative immunoblotting, mass spectrometry and quantitative real-time PCR (qRT-PCR) in CFU-E and H838 cells as well as H838 cells overexpressing human EPOR (H838-HA-hEPOR). The established parsimonious mathematical model was able to simultaneously describe the data sets of CFU-E, H838 and H838-HA-hEPOR cells. Seven cell type-specific parameters were identified that included for example parameters for nuclear translocation of STAT5 and target gene induction. Cell type-specific differences in target gene induction were experimentally validated by qRT-PCR experiments. The systematic identification of pathway differences and sensitivities of EPOR signaling in CFU-E and H838 cells revealed potential targets for intervention to selectively inhibit EPO-induced signaling in the tumor cells but leave the responses in erythroid progenitor cells unaffected. Thus, the proposed modeling strategy can be employed as a general procedure to identify cell type-specific parameters and to recommend treatment strategies for the selective targeting of specific cell types. A major challenge in the development of therapeutic interventions is the selective inhibition of a signal transduction pathway in one cell type such as a cancer cell leaving the other cell type such as a healthy cell as unaffected as possible. Here, we propose a new approach that combines mathematical modeling based on quantitative experimental data with statistical methods. We demonstrate based on simulated data that our approach can determine which parameters are the same and which parameters differ in two exemplary cell types. We compare a lung cancer cell line to the precursor cells of red blood cells. We show that the same signal transduction network induced by erythropoietin (EPO), a hormone that is frequently employed to treat anemia in cancer patients, regulates survival of both cell types. Based on our experimental data in combination with our computational approach, we identify seven cell type-specific differences in this signaling pathway. Our strategy allows predicting therapeutic targets that could be inhibited to interfere with survival of lung cancer cells while leaving production of red blood cells unaffected.
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Affiliation(s)
- Ruth Merkle
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), INF 280, Heidelberg, Germany
- Translational Lung Research Center (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Bernhard Steiert
- Institute of Physics, University of Freiburg, Germany & BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany
| | - Florian Salopiata
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), INF 280, Heidelberg, Germany
- Translational Lung Research Center (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Sofia Depner
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), INF 280, Heidelberg, Germany
- Translational Lung Research Center (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Andreas Raue
- Institute of Physics, University of Freiburg, Germany & BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany
| | - Nao Iwamoto
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), INF 280, Heidelberg, Germany
| | - Max Schelker
- Institute of Physics, University of Freiburg, Germany & BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany
| | - Helge Hass
- Institute of Physics, University of Freiburg, Germany & BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany
| | - Marvin Wäsch
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), INF 280, Heidelberg, Germany
- Translational Lung Research Center (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Martin E. Böhm
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), INF 280, Heidelberg, Germany
| | - Oliver Mücke
- Division Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), INF 280, Heidelberg, Germany
| | - Daniel B. Lipka
- Regulation of Cellular Differentiation Group, Division Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), INF 280, Heidelberg, Germany
| | - Christoph Plass
- Division Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), INF 280, Heidelberg, Germany
| | - Wolf D. Lehmann
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), INF 280, Heidelberg, Germany
| | - Clemens Kreutz
- Institute of Physics, University of Freiburg, Germany & BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany
| | - Jens Timmer
- Institute of Physics, University of Freiburg, Germany & BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany
- * E-mail: (JT); (MS); (UK)
| | - Marcel Schilling
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), INF 280, Heidelberg, Germany
- * E-mail: (JT); (MS); (UK)
| | - Ursula Klingmüller
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), INF 280, Heidelberg, Germany
- Translational Lung Research Center (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
- * E-mail: (JT); (MS); (UK)
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256
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Brandt AP, Gozzi GJ, Pires ADRA, Martinez GR, Dos Santos Canuto AV, Echevarria A, Di Pietro A, Cadena SMSC. Impairment of oxidative phosphorylation increases the toxicity of SYD-1 on hepatocarcinoma cells (HepG2). Chem Biol Interact 2016; 256:154-60. [PMID: 27417255 DOI: 10.1016/j.cbi.2016.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 06/22/2016] [Accepted: 07/07/2016] [Indexed: 12/11/2022]
Abstract
Toxicity of the SYD-1 mesoionic compound (3-[4-chloro-3-nitrophenyl]-1,2,3-oxadiazolium-5-olate) was evaluated on human liver cancer cells (HepG2) grown in either high glucose (HG) or galactose (GAL) medium, and also on suspended cells kept in HG medium. SYD-1 was able to decrease the viability of cultured HepG2 cells in a dose-dependent manner, as assessed by MTT, LDH release and dye with crystal violet assays, but no effect was observed on suspended cells after 1-40 min of treatment. Respiration analysis was performed after 2 min (suspended cells) or 24 h (cultured cells) of treatment: no change was observed in suspended cells, whereas SYD-1 inhibited as well basal, leak and uncoupled states of the respiration in cultured cells with HG medium. These inhibitions were consistent with the decrease in pyruvate level and increase in lactate level. Even more extended results were obtained with HepG2 cells grown in GAL medium where, additionally, the ATP amount was reduced. Furthermore, SYD-1 appears not to be transported by the main ABC multidrug transporters. These results show that SYD-1 is able to change the metabolism of HepG2 cells, and suggest that its cytotoxicity is related to impairment of mitochondrial metabolism. Therefore, we may propose that SYD-1 is a potential candidate for hepatocarcinoma treatment.
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Affiliation(s)
- Anna Paula Brandt
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Gustavo Jabor Gozzi
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | | | - Glaucia Regina Martinez
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | | | - Aurea Echevarria
- Departamento de Química, Universidade Federal Rural do Rio de Janeiro, Rio de Janeiro, Brazil
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257
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Wiśniewski JR, Mann M. A Proteomics Approach to the Protein Normalization Problem: Selection of Unvarying Proteins for MS-Based Proteomics and Western Blotting. J Proteome Res 2016; 15:2321-6. [PMID: 27297043 DOI: 10.1021/acs.jproteome.6b00403] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Proteomics and other protein-based analysis methods such as Western blotting all face the challenge of discriminating changes in the levels of proteins of interest from inadvertent changes in the amount loaded for analysis. Mass-spectrometry-based proteomics can now estimate the relative and absolute amounts of thousands of proteins across diverse biological systems. We reasoned that this new technology could prove useful for selection of very stably expressed proteins that could serve as better loading controls than those traditionally employed. Large-scale proteomic analyses of SDS lysates of cultured cells and tissues revealed deglycase DJ-1 as the protein with the lowest variability in abundance among different cell types in human, mouse, and amphibian cells. The protein constitutes 0.069 ± 0.017% of total cellular protein and occurs at a specific concentration of 34.6 ± 8.7 pmol/mg of total protein. Since DJ-1 is ubiquitous and therefore easily detectable with several peptides, it can be helpful in normalization of proteomic data sets. In addition, DJ-1 appears to be an advantageous loading control for Western blot that is superior to those used commonly used, allowing comparisons between tissues and cells originating from evolutionarily distant vertebrate species. Notably, this is not possible by the detection and quantitation of housekeeping proteins, which are often used in the Western blot technique. The approach introduced here can be applied to select the most appropriate loading controls for MS-based proteomics or Western blotting in any biological system.
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Affiliation(s)
- Jacek R Wiśniewski
- Biochemical Proteomics Group, ‡Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry , 82152 Martinsried, Germany
| | - Matthias Mann
- Biochemical Proteomics Group, ‡Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry , 82152 Martinsried, Germany
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258
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Guo C, Yang K, Brouwer KR, St Claire RL, Brouwer KLR. Prediction of Altered Bile Acid Disposition Due to Inhibition of Multiple Transporters: An Integrated Approach Using Sandwich-Cultured Hepatocytes, Mechanistic Modeling, and Simulation. J Pharmacol Exp Ther 2016; 358:324-33. [PMID: 27233294 DOI: 10.1124/jpet.116.231928] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 05/26/2016] [Indexed: 01/11/2023] Open
Abstract
Transporter-mediated alterations in bile acid disposition may have significant toxicological implications. Current methods to predict interactions are limited by the interplay of multiple transporters, absence of protein in the experimental system, and inaccurate estimates of inhibitor concentrations. An integrated approach was developed to predict altered bile acid disposition due to inhibition of multiple transporters using the model bile acid taurocholate (TCA). TCA pharmacokinetic parameters were estimated by mechanistic modeling using sandwich-cultured human hepatocyte data with protein in the medium. Uptake, basolateral efflux, and biliary clearance estimates were 0.63, 0.034, and 0.074 mL/min/g liver, respectively. Cellular total TCA concentrations (Ct,Cells) were selected as the model output based on sensitivity analysis. Monte Carlo simulations of TCA Ct,Cells in the presence of model inhibitors (telmisartan and bosentan) were performed using inhibition constants for TCA transporters and inhibitor concentrations, including cellular total inhibitor concentrations ([I]t,cell) or unbound concentrations, and cytosolic total or unbound concentrations. For telmisartan, the model prediction was accurate with an average fold error (AFE) of 0.99-1.0 when unbound inhibitor concentration ([I]u) was used; accuracy dropped when total inhibitor concentration ([I]t) was used. For bosentan, AFE was 1.2-1.3 using either [I]u or [I]t This difference was evaluated by sensitivity analysis of the cellular unbound fraction of inhibitor (fu,cell,inhibitor), which revealed higher sensitivity of fu,cell,inhibitor for predicting TCA Ct,Cells when inhibitors exhibited larger ([I]t,cell/IC50) values. In conclusion, this study demonstrated the applicability of a framework to predict hepatocellular bile acid concentrations due to drug-mediated inhibition of transporters using mechanistic modeling and cytosolic or cellular unbound concentrations.
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Affiliation(s)
- Cen Guo
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.G., K.Y., K.L.R.B.); and Qualyst Transporter Solutions, Durham, North Carolina (K.R.B., R.L.S.C.)
| | - Kyunghee Yang
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.G., K.Y., K.L.R.B.); and Qualyst Transporter Solutions, Durham, North Carolina (K.R.B., R.L.S.C.)
| | - Kenneth R Brouwer
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.G., K.Y., K.L.R.B.); and Qualyst Transporter Solutions, Durham, North Carolina (K.R.B., R.L.S.C.)
| | - Robert L St Claire
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.G., K.Y., K.L.R.B.); and Qualyst Transporter Solutions, Durham, North Carolina (K.R.B., R.L.S.C.)
| | - Kim L R Brouwer
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (C.G., K.Y., K.L.R.B.); and Qualyst Transporter Solutions, Durham, North Carolina (K.R.B., R.L.S.C.)
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