1
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Whiteaker JR, Sharma K, Hoffman MA, Kuhn E, Zhao L, Cocco AR, Schoenherr RM, Kennedy JJ, Voytovich U, Lin C, Fang B, Bowers K, Whiteley G, Colantonio S, Bocik W, Roberts R, Hiltke T, Boja E, Rodriguez H, McCormick F, Holderfield M, Carr SA, Koomen JM, Paulovich AG. Targeted mass spectrometry-based assays enable multiplex quantification of receptor tyrosine kinase, MAP Kinase, and AKT signaling. CELL REPORTS METHODS 2021; 1:100015. [PMID: 34671754 PMCID: PMC8525888 DOI: 10.1016/j.crmeth.2021.100015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/16/2021] [Accepted: 05/07/2021] [Indexed: 02/07/2023]
Abstract
SUMMARY A primary goal of the US National Cancer Institute's Ras initiative at the Frederick National Laboratory for Cancer Research is to develop methods to quantify RAS signaling to facilitate development of novel cancer therapeutics. We use targeted proteomics technologies to develop a community resource consisting of 256 validated multiple reaction monitoring (MRM)-based, multiplexed assays for quantifying protein expression and phosphorylation through the receptor tyrosine kinase, MAPK, and AKT signaling networks. As proof of concept, we quantify the response of melanoma (A375 and SK-MEL-2) and colorectal cancer (HCT-116 and HT-29) cell lines to BRAF inhibition by PLX-4720. These assays replace over 60 Western blots with quantitative mass spectrometry-based assays of high molecular specificity and quantitative precision, showing the value of these methods for pharmacodynamic measurements and mechanism of action studies. Methods, fit-for-purpose validation, and results are publicly available as a resource for the community at assays.cancer.gov. MOTIVATION A lack of quantitative, multiplexable assays for phosphosignaling limits comprehensive investigation of aberrant signaling in cancer and evaluation of novel treatments. To alleviate this limitation, we sought to develop assays using targeted mass spectrometry for quantifying protein expression and phosphorylation through the receptor tyrosine kinase, MAPK, and AKT signaling networks. The resulting assays provide a resource for replacing over 60 Western blots in examining cancer signaling and tumor biology with high molecular specificity and quantitative rigor.
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Affiliation(s)
- Jeffrey R. Whiteaker
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Kanika Sharma
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Melissa A. Hoffman
- Proteomics and Metabolomics Core, Department of Molecular Oncology, and Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Eric Kuhn
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Lei Zhao
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Alexandra R. Cocco
- Gillings School of Global Public Health, Kenan-Flagler Business School, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Regine M. Schoenherr
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jacob J. Kennedy
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ulianna Voytovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Chenwei Lin
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Bin Fang
- Proteomics and Metabolomics Core, Department of Molecular Oncology, and Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Kiah Bowers
- Proteomics and Metabolomics Core, Department of Molecular Oncology, and Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Gordon Whiteley
- Antibody Characterization Laboratory, Leidos Biochemical Research Inc, Frederick National Laboratory for Cancer Research ATRF, Frederick, MD 21701, USA
| | - Simona Colantonio
- Antibody Characterization Laboratory, Leidos Biochemical Research Inc, Frederick National Laboratory for Cancer Research ATRF, Frederick, MD 21701, USA
| | - William Bocik
- Antibody Characterization Laboratory, Leidos Biochemical Research Inc, Frederick National Laboratory for Cancer Research ATRF, Frederick, MD 21701, USA
| | - Rhonda Roberts
- Antibody Characterization Laboratory, Leidos Biochemical Research Inc, Frederick National Laboratory for Cancer Research ATRF, Frederick, MD 21701, USA
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Emily Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Frank McCormick
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Matthew Holderfield
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
- Department of Biology, Revolution Medicines, Inc., Redwood City, CA 94063, USA
| | - Steven A. Carr
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - John M. Koomen
- Proteomics and Metabolomics Core, Department of Molecular Oncology, and Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Amanda G. Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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2
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Zhang B, Whiteaker JR, Hoofnagle AN, Baird GS, Rodland KD, Paulovich AG. Clinical potential of mass spectrometry-based proteogenomics. Nat Rev Clin Oncol 2019; 16:256-268. [PMID: 30487530 PMCID: PMC6448780 DOI: 10.1038/s41571-018-0135-7] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cancer genomics research aims to advance personalized oncology by finding and targeting specific genetic alterations associated with cancers. In genome-driven oncology, treatments are selected for individual patients on the basis of the findings of tumour genome sequencing. This personalized approach has prolonged the survival of subsets of patients with cancer. However, many patients do not respond to the predicted therapies based on the genomic profiles of their tumours. Furthermore, studies pairing genomic and proteomic analyses of samples from the same tumours have shown that the proteome contains novel information that cannot be discerned through genomic analysis alone. This observation has led to the concept of proteogenomics, in which both types of data are leveraged for a more complete view of tumour biology that might enable patients to be more successfully matched to effective treatments than they would using genomics alone. In this Perspective, we discuss the added value of proteogenomics over the current genome-driven approach to the clinical characterization of cancers and summarize current efforts to incorporate targeted proteomic measurements based on selected/multiple reaction monitoring (SRM/MRM) mass spectrometry into the clinical laboratory to facilitate clinical proteogenomics.
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Affiliation(s)
- Bing Zhang
- Department of Molecular and Human Genetics, Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Jeffrey R Whiteaker
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Andrew N Hoofnagle
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Geoffrey S Baird
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Cell, Development and Cancer Biology, Oregon Health & Sciences University, Portland, OR, USA
| | - Amanda G Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Division of Medical Oncology, University of Washington School of Medicine, Seattle, WA, USA.
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3
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Voruganti S, Kline JT, Balch MJ, Rogers J, Matts RL, Hartson SD. Proteomic Profiling of Hsp90 Inhibitors. Methods Mol Biol 2018; 1709:139-162. [PMID: 29177657 DOI: 10.1007/978-1-4939-7477-1_11] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Mass spectrometry assays demonstrate that Hsp90 inhibitors alter the expression of approximately one-quarter of the assayable proteome in mammalian cells. These changes are extraordinarily robust and reproducible, making "proteomics profiling" the gold standard for validating the effects of new Hsp90 inhibitors on cultured cells. Proteomics assays can also suggest novel hypotheses regarding drug mechanisms. To assist investigators in adopting this approach, this Chapter provides detailed protocols for conducting simple proteomics assays of Hsp90 inhibition. The protocols present a robust label-free approach that utilizes pre-fractionation of protein samples by SDS-PAGE, thereby providing reasonably good penetration into the proteome while addressing common issues with sample quality. The actual programming and operation of liquid chromatography-tandem mass spectrometers is not covered, but expectations for achievable performance are discussed, as are alternative approaches, common challenges, and software for data analysis.
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Affiliation(s)
- Sudhakar Voruganti
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA.,Bristol-Myers Squibb, Pennington, NJ, USA
| | - Jake T Kline
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Maurie J Balch
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Janet Rogers
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Robert L Matts
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Steven D Hartson
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA.
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4
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Chen Y, Britton D, Wood ER, Brantley S, Fournier M, Wloch M, Williams VL, Johnson J, Magliocco A, Pike I, Koomen JM. Quantification of Breast Cancer Protein Biomarkers at Different Expression Levels in Human Tumors. Methods Mol Biol 2018; 1788:251-268. [PMID: 29243084 PMCID: PMC7771335 DOI: 10.1007/7651_2017_113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Liquid chromatography-selected reaction monitoring (LC-SRM) mass spectrometry has developed into a versatile tool for quantification of proteins with a wide range of applications in basic science, translational research, and clinical patient assessment. This strategy uniquely complements traditional pathology approaches, like hematoxylin and eosin (H&E) staining and immunohistochemistry (IHC). The multiplexing capabilities offered by mass spectrometry are currently unmatched by other techniques. However, quantification of biomarkers in tissue specimens without the other data obtained from H&E-stained slides or IHC, including tumor cellularity or percentage of positively stained cells inter alia, may not provide as much information that is needed to fully understand tumor biology or properly assess the patient. Therefore, additional characterization of the tissue proteome is needed, which in turn requires the ability to assess protein markers across a wide range of expression levels from a single sample. This protocol provides an example of multiplexed analysis in breast tumor tissue quantifying specific biomarkers, specifically estrogen receptor, progesterone receptor, and the HER2 receptor tyrosine kinase, in combination with other proteins that can report on tissue content and other aspects of tumor biology.
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Affiliation(s)
- Yi Chen
- Molecular Oncology/Proteomics SRB3, Moffitt Cancer Center, Tampa, FL, USA
| | | | - Elizabeth R Wood
- Molecular Oncology/Proteomics SRB3, Moffitt Cancer Center, Tampa, FL, USA
| | | | - Michelle Fournier
- Molecular Oncology/Proteomics SRB3, Moffitt Cancer Center, Tampa, FL, USA
| | - Marek Wloch
- Molecular Oncology/Proteomics SRB3, Moffitt Cancer Center, Tampa, FL, USA
| | - Vonetta L Williams
- Molecular Oncology/Proteomics SRB3, Moffitt Cancer Center, Tampa, FL, USA
| | - Joseph Johnson
- Molecular Oncology/Proteomics SRB3, Moffitt Cancer Center, Tampa, FL, USA
| | - Anthony Magliocco
- Molecular Oncology/Proteomics SRB3, Moffitt Cancer Center, Tampa, FL, USA
| | - Ian Pike
- Proteome Sciences, plc, Cobham, UK
| | - John M Koomen
- Molecular Oncology/Proteomics SRB3, Moffitt Cancer Center, Tampa, FL, USA.
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5
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Agyei D, Pan S, Acquah C, Bekhit AEDA, Danquah MK. Structure-informed detection and quantification of peptides in food and biological fluids. J Food Biochem 2017; 43:e12482. [PMID: 31353495 DOI: 10.1111/jfbc.12482] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/08/2017] [Accepted: 11/09/2017] [Indexed: 02/06/2023]
Abstract
Peptides with biological properties, that is, bioactive peptides, are a class of biomolecules whose health-promoting properties are increasingly being exploited in food and health products. However, research on targeted techniques for the detection and quantification of these peptides is still in its infancy. Such information is needed in order to enhance the biological and chemometric characterization of peptides and their subsequent application in the functional food and pharmaceutical industries. In this review, the role of classic techniques such as electrophoretic, chromatographic, and peptide mass spectrometry in the structure-informed detection and quantitation of bioactive peptides are discussed. Prospects for the use of aptamers in the characterization of bioactive peptides are also discussed. PRACTICAL APPLICATIONS: Although bioactive peptides have huge potential applications in the functional foods and health area, there are limited techniques in enhancing throughput detection, quantification, and characterization of these peptides. This review discusses state-of-the-art techniques relevant in complementing bioactive detection and profiling irrespective of the small number of amino acid units. Insights into challenges, possible remedies and prevailing areas requiring thorough research in the extant literature for food chemists and biotechnologists are also presented.
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Affiliation(s)
- Dominic Agyei
- Department of Food Science, University of Otago, Dunedin 9054, New Zealand
| | - Sharadwata Pan
- School of Life Sciences Weihenstephan, Technical University of Munich, Freising 85354, Germany
| | - Caleb Acquah
- Curtin Malaysia Research Institute, Curtin University, Sarawak 98009, Malaysia.,Department of Chemical Engineering, Curtin University, Sarawak 98009, Malaysia
| | | | - Michael K Danquah
- Curtin Malaysia Research Institute, Curtin University, Sarawak 98009, Malaysia.,Department of Chemical Engineering, Curtin University, Sarawak 98009, Malaysia
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6
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Chen Y, Britton D, Wood ER, Brantley S, Magliocco A, Pike I, Koomen JM. Quantitative proteomics of breast tumors: Tissue quality assessment to clinical biomarkers. Proteomics 2017; 17. [PMID: 28127872 DOI: 10.1002/pmic.201600335] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 11/11/2016] [Accepted: 01/23/2017] [Indexed: 01/07/2023]
Abstract
Liquid chromatography-selected reaction monitoring mass spectrometry (LC-SRM) is not only a proven tool for clinical chemistry, but also a versatile method to enhance the capability to quantify biomarkers for tumor biology research. As the treatment of cancer continues to evolve, the ability to assess multiple biomarkers to assign cancer phenotypes based on the genetic background and the signaling of the individual tumor becomes paramount to our ability to treat the patient. In breast cancer, the American Society of Clinical Oncology has defined biomarkers for patient assessment to guide selection of therapy: estrogen receptor, progesterone receptor, and the HER2/Neu receptor tyrosine kinase; therefore, these proteins were selected for LC-SRM assay development. Detailed molecular characterization of these proteins is necessary for patient treatment, so expression and phosphorylation assays have been developed and applied. In addition, other LC-SRM assays were developed to further evaluate tumor biology (e.g. Ki-67 for proliferation and vimentin for tumor aggressiveness related to the epithelial-to-mesenchymal transition). These measurements combined with biomarkers for tissue quality and histological content are implemented in a three-tier multiplexed assay platform, which is translated from cell line models into frozen tumor tissues banked from breast cancer patients.
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Affiliation(s)
- Yi Chen
- Molecular Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | | | | | | | | | - Ian Pike
- Proteome Sciences plc., Cobham, UK
| | - John M Koomen
- Molecular Oncology, Moffitt Cancer Center, Tampa, FL, USA.,Chemical Biology and Molecular Medicine, Moffitt Cancer Center, Tampa, FL, USA
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7
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Frieling JS, Shay G, Izumi V, Aherne ST, Saul RG, Budzevich M, Koomen J, Lynch CC. Matrix metalloproteinase processing of PTHrP yields a selective regulator of osteogenesis, PTHrP 1-17. Oncogene 2017; 36:4498-4507. [PMID: 28368420 DOI: 10.1038/onc.2017.70] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 01/19/2017] [Accepted: 02/21/2017] [Indexed: 01/02/2023]
Abstract
Parathyroid hormone-related protein (PTHrP) is a critical regulator of bone resorption and augments osteolysis in skeletal malignancies. Here we report that the mature PTHrP1-36 hormone is processed by matrix metalloproteinases to yield a stable product, PTHrP1-17. PTHrP1-17 retains the ability to signal through PTH1R to induce calcium flux and ERK phosphorylation but not cyclic AMP production or CREB phosphorylation. Notably, PTHrP1-17 promotes osteoblast migration and mineralization in vitro, and systemic administration of PTHrP1-17 augments ectopic bone formation in vivo. Further, in contrast to PTHrP1-36, PTHrP1-17 does not affect osteoclast formation/function in vitro or in vivo. Finally, immunoprecipitation-mass spectrometry analyses using PTHrP1-17-specific antibodies establish that PTHrP1-17 is indeed generated by cancer cells. Thus, matrix metalloproteinase-directed processing of PTHrP disables the osteolytic functions of the mature hormone to promote osteogenesis, indicating important roles for this circuit in bone remodelling in normal and disease contexts.
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Affiliation(s)
- J S Frieling
- Departments of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - G Shay
- Departments of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - V Izumi
- Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - S T Aherne
- Departments of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - R G Saul
- Antibody Characterization Lab, Leidos Biomedical Research, Frederick, MD, USA
| | - M Budzevich
- Cancer Imaging and Metabolism, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - J Koomen
- Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - C C Lynch
- Departments of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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8
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Faria SS, Morris CFM, Silva AR, Fonseca MP, Forget P, Castro MS, Fontes W. A Timely Shift from Shotgun to Targeted Proteomics and How It Can Be Groundbreaking for Cancer Research. Front Oncol 2017; 7:13. [PMID: 28265552 PMCID: PMC5316539 DOI: 10.3389/fonc.2017.00013] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 01/17/2017] [Indexed: 01/10/2023] Open
Abstract
The fact that cancer is a leading cause of death all around the world has naturally sparked major efforts in the pursuit of novel and more efficient biomarkers that could better serve as diagnostic tools, prognostic predictors, or therapeutical targets in the battle against this type of disease. Mass spectrometry-based proteomics has proven itself as a robust and logical alternative to the immuno-based methods that once dominated the field. Nevertheless, intrinsic limitations of classic proteomic approaches such as the natural gap between shotgun discovery-based methods and clinically applicable results have called for the implementation of more direct, hypothesis-based studies such as those made available through targeted approaches, that might be able to streamline biomarker discovery and validation as a means to increase survivability of affected patients. In fact, the paradigm shifting potential of modern targeted proteomics applied to cancer research can be demonstrated by the large number of advancements and increasing examples of new and more useful biomarkers found during the course of this review in different aspects of cancer research. Out of the many studies dedicated to cancer biomarker discovery, we were able to devise some clear trends, such as the fact that breast cancer is the most common type of tumor studied and that most of the research for any given type of cancer is focused on the discovery diagnostic biomarkers, with the exception of those that rely on samples other than plasma and serum, which are generally aimed toward prognostic markers. Interestingly, the most common type of targeted approach is based on stable isotope dilution-selected reaction monitoring protocols for quantification of the target molecules. Overall, this reinforces that notion that targeted proteomics has already started to fulfill its role as a groundbreaking strategy that may enable researchers to catapult the number of viable, effective, and validated biomarkers in cancer clinical practice.
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Affiliation(s)
- Sara S Faria
- Mastology Program, Federal University of Uberlandia (UFU) , Uberlandia , Brazil
| | - Carlos F M Morris
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia , Brasília , Brazil
| | - Adriano R Silva
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia , Brasília , Brazil
| | - Micaella P Fonseca
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, Brazil; Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Patrice Forget
- Department of Anesthesiology and Perioperative Medicine, Universitair Ziekenhuis Brussel, Vrije Universiteit of Brussel , Brussels , Belgium
| | - Mariana S Castro
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia , Brasília , Brazil
| | - Wagner Fontes
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia , Brasília , Brazil
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9
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Multiplexed Liquid Chromatography-Multiple Reaction Monitoring Mass Spectrometry Quantification of Cancer Signaling Proteins. Methods Mol Biol 2017; 1647:19-45. [PMID: 28808993 DOI: 10.1007/978-1-4939-7201-2_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Quantitative evaluation of protein expression across multiple cancer-related signaling pathways (e.g., Wnt/β-catenin, TGF-β, receptor tyrosine kinases (RTK), MAP kinases, NF-κB, and apoptosis) in tumor tissues may enable the development of a molecular profile for each individual tumor that can aid in the selection of appropriate targeted cancer therapies. Here, we describe the development of a broadly applicable protocol to develop and implement quantitative mass spectrometry assays using cell line models and frozen tissue specimens from colon cancer patients. Cell lines are used to develop peptide-based assays for protein quantification, which are incorporated into a method based on SDS-PAGE protein fractionation, in-gel digestion, and liquid chromatography-multiple reaction monitoring mass spectrometry (LC-MRM/MS). This analytical platform is then applied to frozen tumor tissues. This protocol can be broadly applied to the study of human disease using multiplexed LC-MRM assays.
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10
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Ippoliti PJ, Kuhn E, Mani DR, Fagbami L, Keshishian H, Burgess MW, Jaffe JD, Carr SA. Automated Microchromatography Enables Multiplexing of Immunoaffinity Enrichment of Peptides to Greater than 150 for Targeted MS-Based Assays. Anal Chem 2016; 88:7548-55. [PMID: 27321643 DOI: 10.1021/acs.analchem.6b00946] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Immunoaffinity enrichment of peptides coupled with analysis by stable isotope dilution multiple reaction mass spectrometry has been shown to have analytical performance and detection limits suitable for many biomarker verification studies and biological applications. Prior studies have shown that antipeptide antibodies can be multiplexed up to 50 in a single assay without significant loss of performance. Achieving higher multiplex levels is relevant to all studies involving precious biological material as this minimizes the amount of sample that must be consumed to measure a given set of analytes and reduces the assay cost per analyte. Here we developed automated methods employing the Agilent AssayMAP Bravo microchromatography platform and used these methods to characterize the performance of immunoaffinity enrichment of peptides up to multiplex levels of 172. Median capture efficiency for the target peptides remained high (88%) even at levels of 150-plex and declined to 70% at 172-plex compared to antibody performance observed at standard lower multiplex levels (n = 25). Subsequently, we developed and analytically characterized a multiplexed immuno-multiple reaction monitoring-mass spectrometry (immuno-MRM-MS) assay (n = 110) and applied it to measure candidate protein biomarkers of cardiovascular disease in plasma of patients undergoing planned myocardial infarction. The median lower limit of detection of all peptides was 71.5 amol/μL (nM), and the coefficient of variation (CV) was less than 15% at the lower limit of quantification. The results demonstrate that high multiplexed immuno-MRM-MS assays are readily achievable using the optimized sample processing and peptide capture methods described here.
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Affiliation(s)
- Paul J Ippoliti
- Broad Institute of MIT and Harvard , Cambridge, Massachusetts 02142, United States
| | - Eric Kuhn
- Broad Institute of MIT and Harvard , Cambridge, Massachusetts 02142, United States
| | - D R Mani
- Broad Institute of MIT and Harvard , Cambridge, Massachusetts 02142, United States
| | - Lola Fagbami
- Broad Institute of MIT and Harvard , Cambridge, Massachusetts 02142, United States
| | - Hasmik Keshishian
- Broad Institute of MIT and Harvard , Cambridge, Massachusetts 02142, United States
| | - Michael W Burgess
- Broad Institute of MIT and Harvard , Cambridge, Massachusetts 02142, United States
| | - Jacob D Jaffe
- Broad Institute of MIT and Harvard , Cambridge, Massachusetts 02142, United States
| | - Steven A Carr
- Broad Institute of MIT and Harvard , Cambridge, Massachusetts 02142, United States
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11
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Chen S, Fisher RC, Signs S, Molina LA, Shenoy AK, Lopez MC, Baker HV, Koomen JM, Chen Y, Gittleman H, Barnholtz-Sloan J, Berg A, Appelman HD, Huang EH. Inhibition of PI3K/Akt/mTOR signaling in PI3KR2-overexpressing colon cancer stem cells reduces tumor growth due to apoptosis. Oncotarget 2016; 8:50476-50488. [PMID: 28881576 PMCID: PMC5584153 DOI: 10.18632/oncotarget.9919] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/19/2016] [Indexed: 01/06/2023] Open
Abstract
In sporadic colon cancer, colon cancer stem cells (CCSCs) initiate tumorigenesis and may contribute to late disease recurrences and metastases. We previously showed that aldehyde dehydrogenase (ALDH) activity (as indicated by the ALDEFLUOR® assay) is an effective marker for highly enriching CCSCs for further evaluation. Here, we used comparative transcriptome and proteome approaches to identify signaling pathways overrepresented in the CCSC population. We found overexpression of several components of the phosphoinositide 3-kinase (PI3K)/Akt/mechanistic target of rapamycin (mTOR) signaling pathway, including PI3KR2, a regulatory subunit of PI3K. LY294002, a PI3K inhibitor, defined the contribution of the PI3K/Akt/mTOR signaling pathway in CCSCs. LY294002-treated CCSCs showed decreases in proliferation, sphere formation and self-renewal, in phosphorylation-dependent activation of Akt, and in expression of cyclin D1. Inhibition of PI3K in vivo reduced tumorigenicity, increased detection of cleaved caspase 3, an indicator of apoptosis, and elevated expression of the inflammatory chemokine, CXCL8. Collectively, these results indicate that PI3K/Akt/mTOR signaling controls CCSC proliferation and CCSC survival, and suggests that it would be useful to develop therapeutic agents that target this signaling pathway.
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Affiliation(s)
- Sugong Chen
- Department of Surgery, University of Florida, Gainesville, Florida 32610, USA
| | - Robert C Fisher
- Department of Surgery, University of Florida, Gainesville, Florida 32610, USA.,Department of Stem Cell Biology and Regenerative Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio 44195, USA
| | - Steven Signs
- Department of Stem Cell Biology and Regenerative Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio 44195, USA
| | - L Alex Molina
- Department of Stem Cell Biology and Regenerative Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio 44195, USA
| | - Anitha K Shenoy
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida 32610, USA
| | - Maria-Cecilia Lopez
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida 32610, USA
| | - Henry V Baker
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida 32610, USA
| | - John M Koomen
- Molecular Oncology and Proteomics, SRB3, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA
| | - Yi Chen
- Molecular Oncology and Proteomics, SRB3, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA
| | - Haley Gittleman
- Bioinformatics, Case Comprehensive Cancer Center, Cleveland, Ohio 44106, USA
| | | | - Annamarie Berg
- Department of Stem Cell Biology and Regenerative Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio 44195, USA
| | - Henry D Appelman
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Emina H Huang
- Department of Surgery, University of Florida, Gainesville, Florida 32610, USA.,Department of Stem Cell Biology and Regenerative Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio 44195, USA
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12
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Sabbagh B, Mindt S, Neumaier M, Findeisen P. Clinical applications of MS-based protein quantification. Proteomics Clin Appl 2016; 10:323-45. [DOI: 10.1002/prca.201500116] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/18/2015] [Accepted: 12/30/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Bassel Sabbagh
- Institute for Clinical Chemistry; Medical Faculty Mannheim of the University of Heidelberg; University Hospital Mannheim; Mannheim Germany
| | - Sonani Mindt
- Institute for Clinical Chemistry; Medical Faculty Mannheim of the University of Heidelberg; University Hospital Mannheim; Mannheim Germany
| | - Michael Neumaier
- Institute for Clinical Chemistry; Medical Faculty Mannheim of the University of Heidelberg; University Hospital Mannheim; Mannheim Germany
| | - Peter Findeisen
- Institute for Clinical Chemistry; Medical Faculty Mannheim of the University of Heidelberg; University Hospital Mannheim; Mannheim Germany
- MVZ Labor Dr. Limbach und Kollegen; Heidelberg Germany
- Working Group Proteomics of the German United Society for Clinical Chemistry and Laboratory Medicine e.V. (DGKL); Bonn Germany
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13
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Fedorenko IV, Abel EV, Koomen JM, Fang B, Wood ER, Chen YA, Fisher KJ, Iyengar S, Dahlman KB, Wargo JA, Flaherty KT, Sosman JA, Sondak VK, Messina JL, Gibney GT, Smalley KS. Fibronectin induction abrogates the BRAF inhibitor response of BRAF V600E/PTEN-null melanoma cells. Oncogene 2016; 35:1225-35. [PMID: 26073081 PMCID: PMC4679729 DOI: 10.1038/onc.2015.188] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 03/30/2015] [Accepted: 04/28/2015] [Indexed: 12/30/2022]
Abstract
The mechanisms by which some melanoma cells adapt to Serine/threonine-protein kinase B-Raf (BRAF) inhibitor therapy are incompletely understood. In the present study, we used mass spectrometry-based phosphoproteomics to determine how BRAF inhibition remodeled the signaling network of melanoma cell lines that were BRAF mutant and PTEN null. Short-term BRAF inhibition was associated with marked changes in fibronectin-based adhesion signaling that were PTEN dependent. These effects were recapitulated through BRAF siRNA knockdown and following treatment with chemotherapeutic drugs. Increased fibronectin expression was also observed in mouse xenograft models as well as specimens from melanoma patients undergoing BRAF inhibitor treatment. Analysis of a melanoma tissue microarray showed loss of PTEN expression to predict for a lower overall survival, with a trend for even lower survival being seen when loss of fibronectin was included in the analysis. Mechanistically, the induction of fibronectin limited the responses of these PTEN-null melanoma cell lines to vemurafenib, with enhanced cytotoxicity observed following the knockdown of either fibronectin or its receptor α5β1 integrin. This in turn abrogated the cytotoxic response to BRAF inhibition via increased AKT signaling, which prevented the induction of cell death by maintaining the expression of the pro-survival protein Mcl-1. The protection conveyed by the induction of FN expression could be overcome through combined treatment with a BRAF and PI3K inhibitor.
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Affiliation(s)
- Inna V. Fedorenko
- The Department of Molecular Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612
| | - Ethan V. Abel
- Department of Cancer Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA, 19107, USA
| | - John M. Koomen
- The Department of Molecular Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612
| | - Bin Fang
- Department of Proteomics, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612
| | - Elizabeth R. Wood
- The Department of Molecular Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612
- Department of Proteomics, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612
| | - Y. Ann Chen
- Department of Biostatistics and Bioinformatics, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612
| | - Kate J. Fisher
- Department of Biostatistics and Bioinformatics, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612
| | - Sanjana Iyengar
- The Department of Cutaneous Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612
| | - Kimberly B. Dahlman
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2220 Pierce Avenue, 777 Research Building, Nashville, TN 37232
| | | | | | - Jeffrey A. Sosman
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2220 Pierce Avenue, 777 Research Building, Nashville, TN 37232
| | - Vernon K. Sondak
- The Department of Cutaneous Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612
| | - Jane L. Messina
- The Department of Cutaneous Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612
| | - Geoffrey T. Gibney
- The Department of Cutaneous Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612
| | - Keiran S.M. Smalley
- The Department of Molecular Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612
- The Department of Cutaneous Oncology, The Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612
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14
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Whiteaker JR, Halusa GN, Hoofnagle AN, Sharma V, MacLean B, Yan P, Wrobel JA, Kennedy J, Mani DR, Zimmerman LJ, Meyer MR, Mesri M, Boja E, Carr SA, Chan DW, Chen X, Chen J, Davies SR, Ellis MJC, Fenyö D, Hiltke T, Ketchum KA, Kinsinger C, Kuhn E, Liebler DC, Liu T, Loss M, MacCoss MJ, Qian WJ, Rivers R, Rodland KD, Ruggles KV, Scott MG, Smith RD, Thomas S, Townsend RR, Whiteley G, Wu C, Zhang H, Zhang Z, Rodriguez H, Paulovich AG. Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays. Methods Mol Biol 2016; 1410:223-36. [PMID: 26867747 DOI: 10.1007/978-1-4939-3524-6_13] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the National Cancer Institute (NCI) has launched an Assay Portal (http://assays.cancer.gov) to serve as an open-source repository of well-characterized targeted proteomic assays. The portal is designed to curate and disseminate highly characterized, targeted mass spectrometry (MS)-based assays by providing detailed assay performance characterization data, standard operating procedures, and access to reagents. Assay content is accessed via the portal through queries to find assays targeting proteins associated with specific cellular pathways, protein complexes, or specific chromosomal regions. The position of the peptide analytes for which there are available assays are mapped relative to other features of interest in the protein, such as sequence domains, isoforms, single nucleotide polymorphisms, and posttranslational modifications. The overarching goals are to enable robust quantification of all human proteins and to standardize the quantification of targeted MS-based assays to ultimately enable harmonization of results over time and across laboratories.
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Affiliation(s)
- Jeffrey R Whiteaker
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, N., Seattle, WA, 98109, USA
| | - Goran N Halusa
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, USA
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Vagisha Sharma
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Brendan MacLean
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Ping Yan
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, N., Seattle, WA, 98109, USA
| | - John A Wrobel
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Jacob Kennedy
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, N., Seattle, WA, 98109, USA
| | - D R Mani
- Broad Institute, Cambridge, MA, USA
| | - Lisa J Zimmerman
- Department of Biochemistry, Jim Ayers Institute for Precancer Detection & Diagnosis, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Matthew R Meyer
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, USA
| | - Emily Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, USA
| | | | - Daniel W Chan
- Clinical Chemistry Division, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xian Chen
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Jing Chen
- Clinical Chemistry Division, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sherri R Davies
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Matthew J C Ellis
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - David Fenyö
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, USA
| | | | - Chris Kinsinger
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, USA
| | | | - Daniel C Liebler
- Department of Biochemistry, Jim Ayers Institute for Precancer Detection & Diagnosis, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Michael Loss
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, USA
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Robert Rivers
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kelly V Ruggles
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Mitchell G Scott
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Richard D Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Stefani Thomas
- Clinical Chemistry Division, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - R Reid Townsend
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Gordon Whiteley
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, USA
| | - Chaochao Wu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Hui Zhang
- Clinical Chemistry Division, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zhen Zhang
- Clinical Chemistry Division, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, USA
| | - Amanda G Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, N., Seattle, WA, 98109, USA.
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15
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Chronic acidosis in the tumour microenvironment selects for overexpression of LAMP2 in the plasma membrane. Nat Commun 2015; 6:8752. [PMID: 26658462 PMCID: PMC4682176 DOI: 10.1038/ncomms9752] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 09/22/2015] [Indexed: 12/18/2022] Open
Abstract
Early cancers are avascular and hence, profoundly acidic. Pre-malignant cells must adapt to acidosis to thrive in this hostile microenvironment. Here, we investigate MCF-7 cells that are adapted to grow in acidic conditions using SILAC proteomics and we reveal a significant upregulation of lysosomal proteins. Prominent among these is LAMP2 that functions to protect lysosomal membranes from acid proteolysis. LAMP2 upregulation by acidosis is confirmed both in vitro and in vivo. Furthermore, we show that the depletion of LAMP2 is sufficient to increase acidosis-mediated toxicity. In breast cancer patient samples, there is a high correlation of LAMP2 mRNA and protein expression with progression. We also observe that LAMP2 is located at the plasma membrane in clinical samples and this redistribution is acid-induced in vitro. Our findings suggest a potential adaptive mechanism, wherein cells chronically exposed to an acidic environment translocate lysosomal proteins to their surface, thus protecting the plasmalemma from acid-induced hydrolysis. The protein LAMP2 functions to protect lysosomal membranes from acid proteolysis. In this study, the authors show that malignant cells adapt to the acidic tumour microenvironment by redirecting LAMP2 from lysosomes to the plasma membrane.
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16
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Ebhardt HA, Root A, Sander C, Aebersold R. Applications of targeted proteomics in systems biology and translational medicine. Proteomics 2015; 15:3193-208. [PMID: 26097198 PMCID: PMC4758406 DOI: 10.1002/pmic.201500004] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 04/27/2015] [Accepted: 06/09/2015] [Indexed: 01/28/2023]
Abstract
Biological systems are composed of numerous components of which proteins are of particularly high functional significance. Network models are useful abstractions for studying these components in context. Network representations display molecules as nodes and their interactions as edges. Because they are difficult to directly measure, functional edges are frequently inferred from suitably structured datasets consisting of the accurate and consistent quantification of network nodes under a multitude of perturbed conditions. For the precise quantification of a finite list of proteins across a wide range of samples, targeted proteomics exemplified by selected/multiple reaction monitoring (SRM, MRM) mass spectrometry has proven useful and has been applied to a variety of questions in systems biology and clinical studies. Here, we survey the literature of studies using SRM-MS in systems biology and clinical proteomics. Systems biology studies frequently examine fundamental questions in network biology, whereas clinical studies frequently focus on biomarker discovery and validation in a variety of diseases including cardiovascular disease and cancer. Targeted proteomics promises to advance our understanding of biological networks and the phenotypic significance of specific network states and to advance biomarkers into clinical use.
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Affiliation(s)
- H Alexander Ebhardt
- Department of Biology, Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Alex Root
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medical College, New York, NY, USA
| | - Chris Sander
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
- Faculty of Science, University of Zurich, Zurich, Switzerland
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17
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Mustafa GM, Larry D, Petersen JR, Elferink CJ. Targeted proteomics for biomarker discovery and validation of hepatocellular carcinoma in hepatitis C infected patients. World J Hepatol 2015; 7:1312-1324. [PMID: 26052377 PMCID: PMC4450195 DOI: 10.4254/wjh.v7.i10.1312] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 10/24/2014] [Accepted: 03/09/2015] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC)-related mortality is high because early detection modalities are hampered by inaccuracy, expense and inherent procedural risks. Thus there is an urgent need for minimally invasive, highly specific and sensitive biomarkers that enable early disease detection when therapeutic intervention remains practical. Successful therapeutic intervention is predicated on the ability to detect the cancer early. Similar unmet medical needs abound in most fields of medicine and require novel methodological approaches. Proteomic profiling of body fluids presents a sensitive diagnostic tool for early cancer detection. Here we describe such a strategy of comparative proteomics to identify potential serum-based biomarkers to distinguish high-risk chronic hepatitis C virus infected patients from HCC patients. In order to compensate for the extraordinary dynamic range in serum proteins, enrichment methods that compress the dynamic range without surrendering proteome complexity can help minimize the problems associated with many depletion methods. The enriched serum can be resolved using 2D-difference in-gel electrophoresis and the spots showing statistically significant changes selected for identification by liquid chromatography-tandem mass spectrometry. Subsequent quantitative verification and validation of these candidate biomarkers represent an obligatory and rate-limiting process that is greatly enabled by selected reaction monitoring (SRM). SRM is a tandem mass spectrometry method suitable for identification and quantitation of target peptides within complex mixtures independent on peptide-specific antibodies. Ultimately, multiplexed SRM and dynamic multiple reaction monitoring can be utilized for the simultaneous analysis of a biomarker panel derived from support vector machine learning approaches, which allows monitoring a specific disease state such as early HCC. Overall, this approach yields high probability biomarkers for clinical validation in large patient cohorts and represents a strategy extensible to many diseases.
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18
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López Villar E, Madero L, A López-Pascual J, C Cho W. Study of phosphorylation events for cancer diagnoses and treatment. Clin Transl Med 2015; 4:59. [PMID: 26055493 PMCID: PMC4460185 DOI: 10.1186/s40169-015-0059-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 05/19/2015] [Indexed: 02/07/2023] Open
Abstract
The activation of signaling cascades in response to extracellular and intracellular stimuli to control cell growth, proliferation and survival, is orchestrated by protein kinases via phosphorylation. A critical issue is the study of the mechanisms of cancer cells for the development of more effective drugs. With the application of the new proteomic technologies, together with the advancement in the sequencing of the human proteome, patients will therefore be benefited by the discovery of novel therapeutic and/or diagnostic protein targets. Furthermore, the advances in proteomic approaches and the Human Proteome Organization (HUPO) have opened a new door which is helpful in the identification of patients at risk and towards improving current therapies. Modification of the signaling-networks via mutations or abnormal protein expression underlies the cause or consequence of many diseases including cancer. Resulting data is used to reveal connections between genes proteins and compounds and the related molecular pathways for underlining disease states. As a delegate of HUPO, for human proteome on children assays and studies, we, at Hospital Universitario Niño Jesús, are seeking to support the human proteome in this context. Clinical goals have to be clearly established and proteomics experts have to set up the appropriate proteomic strategy, which coupled to bioinformatics will make it possible to achieve new therapies for patients with poor prognosis. We envision to combine our up-coming data to the HUPO organization in order to support international efforts to advance the cure of cancer disease.
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Affiliation(s)
- Elena López Villar
- Oncohematology of Children Department, Hospital Universitario Infantil Niño Jesús, Av. Menéndez Pelayo 65, Madrid, Spain,
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Parker SJ, Raedschelders K, Van Eyk JE. Emerging proteomic technologies for elucidating context-dependent cellular signaling events: A big challenge of tiny proportions. Proteomics 2015; 15:1486-502. [PMID: 25545106 DOI: 10.1002/pmic.201400448] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 10/31/2014] [Accepted: 12/23/2014] [Indexed: 12/11/2022]
Abstract
Aberrant cell signaling events either drive or compensate for nearly all pathologies. A thorough description and quantification of maladaptive signaling flux in disease is a critical step in drug development, and complex proteomic approaches can provide valuable mechanistic insights. Traditional proteomics-based signaling analyses rely heavily on in vitro cellular monoculture. The characterization of these simplified systems generates a rich understanding of the basic components and complex interactions of many signaling networks, but they cannot capture the full complexity of the microenvironments in which pathologies are ultimately made manifest. Unfortunately, techniques that can directly interrogate signaling in situ often yield mass-limited starting materials that are incompatible with traditional proteomics workflows. This review provides an overview of established and emerging techniques that are applicable to context-dependent proteomics. Analytical approaches are illustrated through recent proteomics-based studies in which selective sample acquisition strategies preserve context-dependent information, and where the challenge of minimal starting material is met by optimized sensitivity and coverage. This review is organized into three major technological themes: (i) LC methods in line with MS; (ii) antibody-based approaches; (iii) MS imaging with a discussion of data integration and systems modeling. Finally, we conclude with future perspectives and implications of context-dependent proteomics.
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Affiliation(s)
- Sarah J Parker
- Department of Medicine, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA; Advanced Clinical Biosystems Research Institute, Los Angeles, CA, USA; Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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20
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Remily-Wood ER, Benson K, Baz RC, Chen YA, Hussein M, Hartley-Brown MA, Sprung RW, Perez B, Liu RZ, Yoder SJ, Teer JK, Eschrich SA, Koomen JM. Quantification of peptides from immunoglobulin constant and variable regions by LC-MRM MS for assessment of multiple myeloma patients. Proteomics Clin Appl 2014; 8:783-95. [PMID: 24723328 DOI: 10.1002/prca.201300077] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 03/05/2014] [Accepted: 04/03/2014] [Indexed: 12/29/2022]
Abstract
PURPOSE Quantitative MS assays for Igs are compared with existing clinical methods in samples from patients with plasma cell dyscrasias, for example, multiple myeloma (MM). EXPERIMENTAL DESIGN Using LC-MS/MS data, Ig constant region peptides, and transitions were selected for LC-MRM MS. Quantitative assays were used to assess Igs in serum from 83 patients. RNA sequencing and peptide-based LC-MRM are used to define peptides for quantification of the disease-specific Ig. RESULTS LC-MRM assays quantify serum levels of Igs and their isoforms (IgG1-4, IgA1-2, IgM, IgD, and IgE, as well as kappa (κ) and lambda (λ) light chains). LC-MRM quantification has been applied to single samples from a patient cohort and a longitudinal study of an IgE patient undergoing treatment, to enable comparison with existing clinical methods. Proof-of-concept data for defining and monitoring variable region peptides are provided using the H929 MM cell line and two MM patients. CONCLUSIONS AND CLINICAL RELEVANCE LC-MRM assays targeting constant region peptides determine the type and isoform of the involved Ig and quantify its expression; the LC-MRM approach has improved sensitivity compared with the current clinical method, but slightly higher inter-assay variability. Detection of variable region peptides is a promising way to improve Ig quantification, which could produce a dramatic increase in sensitivity over existing methods, and could further complement current clinical techniques.
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21
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Whiteaker JR, Halusa GN, Hoofnagle AN, Sharma V, MacLean B, Yan P, Wrobel JA, Kennedy J, Mani DR, Zimmerman LJ, Meyer MR, Mesri M, Rodriguez H, Paulovich AG. CPTAC Assay Portal: a repository of targeted proteomic assays. Nat Methods 2014; 11:703-4. [PMID: 24972168 DOI: 10.1038/nmeth.3002] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Jeffrey R Whiteaker
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Goran N Halusa
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Vagisha Sharma
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Brendan MacLean
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Ping Yan
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - John A Wrobel
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Jacob Kennedy
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - D R Mani
- Broad Institute, Cambridge, Massachusetts, USA
| | - Lisa J Zimmerman
- Department of Biochemistry and Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Matthew R Meyer
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, Maryland, USA
| | | | - Amanda G Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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22
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Detection and quantification of plasma amyloid-β by selected reaction monitoring mass spectrometry. Anal Chim Acta 2014; 840:1-9. [PMID: 25086887 DOI: 10.1016/j.aca.2014.06.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 05/29/2014] [Accepted: 06/16/2014] [Indexed: 01/25/2023]
Abstract
Amyloid-β (Aβ) in human plasma was detected and quantified by an antibody-free method, selected reaction monitoring mass spectrometry (SRM-MS) in the current study. Due to its low abundance, SRM-based quantification in 10 μL plasma was a challenge. Prior to SRM analysis, human plasma proteins as a whole were digested by trypsin and high pH reversed-phase liquid chromatography (RPLC) was used to fractionate the tryptic digests and to collect peptides, Aβ(1-5), Aβ(6-16), Aβ(17-28) and Aβ(29-40(42)) of either Aβ(1-40) or Aβ(1-42). Among those peptides, Aβ(17-28) was selected as a surrogate to measure the total Aβ level. Human plasma samples obtained from triplicate sample preparations were analyzed, obtaining 4.20 ng mL(-1) with a CV of 25.3%. Triplicate measurements for each sample preparation showed CV of <5%. Limit of quantification was obtained as 132 pM, which corresponded to 570 pg mL(-1) of Aβ(1-40). Until now, most quantitative measurements of Aβ in plasma or cerebrospinal fluid have required antibody-based immunoassays. Since quantification of Aβ by immunoassays is highly dependent on the extent of epitope exposure due to aggregation or plasma protein binding, it is difficult to accurately measure the actual concentration of Aβ in plasma. Our diagnostic method based on SRM using a surrogate peptide of Aβ is promising in that actual amounts of total Aβ can be measured regardless of the conformational status of the biomarker.
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23
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Rebecca VW, Wood E, Fedorenko IV, Paraiso KHT, Haarberg HE, Chen Y, Xiang Y, Sarnaik A, Gibney GT, Sondak VK, Koomen JM, Smalley KSM. Evaluating melanoma drug response and therapeutic escape with quantitative proteomics. Mol Cell Proteomics 2014; 13:1844-54. [PMID: 24760959 DOI: 10.1074/mcp.m113.037424] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The evolution of cancer therapy into complex regimens with multiple drugs requires novel approaches for the development and evaluation of companion biomarkers. Liquid chromatography-multiple reaction monitoring mass spectrometry (LC-MRM) is a versatile platform for biomarker measurement. In this study, we describe the development and use of the LC-MRM platform to study the adaptive signaling responses of melanoma cells to inhibitors of HSP90 (XL888) and MEK (AZD6244). XL888 had good anti-tumor activity against NRAS mutant melanoma cell lines as well as BRAF mutant cells with acquired resistance to BRAF inhibitors both in vitro and in vivo. LC-MRM analysis showed HSP90 inhibition to be associated with decreased expression of multiple receptor tyrosine kinases, modules in the PI3K/AKT/mammalian target of rapamycin pathway, and the MAPK/CDK4 signaling axis in NRAS mutant melanoma cell lines and the inhibition of PI3K/AKT signaling in BRAF mutant melanoma xenografts with acquired vemurafenib resistance. The LC-MRM approach targeting more than 80 cancer signaling proteins was highly sensitive and could be applied to fine needle aspirates from xenografts and clinical melanoma specimens (using 50 μg of total protein). We further showed MEK inhibition to be associated with signaling through the NFκB and WNT signaling pathways, as well as increased receptor tyrosine kinase expression and activation. Validation studies identified PDGF receptor β signaling as a potential escape mechanism from MEK inhibition, which could be overcome through combined use of AZD6244 and the PDGF receptor inhibitor, crenolanib. Together, our studies show LC-MRM to have unique value as a platform for the systems level understanding of the molecular mechanisms of drug response and therapeutic escape. This work provides the proof-of-principle for the future development of LC-MRM assays for monitoring drug responses in the clinic.
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Affiliation(s)
| | | | | | | | | | - Yi Chen
- From the ‡Departments of Molecular Oncology
| | - Yun Xiang
- From the ‡Departments of Molecular Oncology
| | | | | | | | - John M Koomen
- From the ‡Departments of Molecular Oncology, ‖Chemical Biology and Molecular Medicine, Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
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24
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Mass spectrometry based biomarker discovery, verification, and validation--quality assurance and control of protein biomarker assays. Mol Oncol 2014; 8:840-58. [PMID: 24713096 DOI: 10.1016/j.molonc.2014.03.006] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Accepted: 03/10/2014] [Indexed: 12/17/2022] Open
Abstract
In its early years, mass spectrometry (MS)-based proteomics focused on the cataloging of proteins found in different species or different tissues. By 2005, proteomics was being used for protein quantitation, typically based on "proteotypic" peptides which act as surrogates for the parent proteins. Biomarker discovery is usually done by non-targeted "shotgun" proteomics, using relative quantitation methods to determine protein expression changes that correlate with disease (output given as "up-or-down regulation" or "fold-increases"). MS-based techniques can also perform "absolute" quantitation which is required for clinical applications (output given as protein concentrations). Here we describe the differences between these methods, factors that affect the precision and accuracy of the results, and some examples of recent studies using MS-based proteomics to verify cancer-related biomarkers.
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25
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Carr SA, Abbatiello SE, Ackermann BL, Borchers C, Domon B, Deutsch EW, Grant RP, Hoofnagle AN, Hüttenhain R, Koomen JM, Liebler DC, Liu T, MacLean B, Mani DR, Mansfield E, Neubert H, Paulovich AG, Reiter L, Vitek O, Aebersold R, Anderson L, Bethem R, Blonder J, Boja E, Botelho J, Boyne M, Bradshaw RA, Burlingame AL, Chan D, Keshishian H, Kuhn E, Kinsinger C, Lee JS, Lee SW, Moritz R, Oses-Prieto J, Rifai N, Ritchie J, Rodriguez H, Srinivas PR, Townsend RR, Van Eyk J, Whiteley G, Wiita A, Weintraub S. Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach. Mol Cell Proteomics 2014; 13:907-17. [PMID: 24443746 PMCID: PMC3945918 DOI: 10.1074/mcp.m113.036095] [Citation(s) in RCA: 431] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 01/14/2014] [Indexed: 12/25/2022] Open
Abstract
Adoption of targeted mass spectrometry (MS) approaches such as multiple reaction monitoring (MRM) to study biological and biomedical questions is well underway in the proteomics community. Successful application depends on the ability to generate reliable assays that uniquely and confidently identify target peptides in a sample. Unfortunately, there is a wide range of criteria being applied to say that an assay has been successfully developed. There is no consensus on what criteria are acceptable and little understanding of the impact of variable criteria on the quality of the results generated. Publications describing targeted MS assays for peptides frequently do not contain sufficient information for readers to establish confidence that the tests work as intended or to be able to apply the tests described in their own labs. Guidance must be developed so that targeted MS assays with established performance can be made widely distributed and applied by many labs worldwide. To begin to address the problems and their solutions, a workshop was held at the National Institutes of Health with representatives from the multiple communities developing and employing targeted MS assays. Participants discussed the analytical goals of their experiments and the experimental evidence needed to establish that the assays they develop work as intended and are achieving the required levels of performance. Using this "fit-for-purpose" approach, the group defined three tiers of assays distinguished by their performance and extent of analytical characterization. Computational and statistical tools useful for the analysis of targeted MS results were described. Participants also detailed the information that authors need to provide in their manuscripts to enable reviewers and readers to clearly understand what procedures were performed and to evaluate the reliability of the peptide or protein quantification measurements reported. This paper presents a summary of the meeting and recommendations.
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Affiliation(s)
- Steven A. Carr
- From the ‡Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | | | | | - Bruno Domon
- ‖Luxembourg Clinical Proteomics Center, Luxembourg
| | | | | | | | - Ruth Hüttenhain
- ¶¶Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- ‖‖University of California San Francisco, California
| | | | | | - Tao Liu
- Pacific Northwest National Laboratory, Richland, Washington
| | | | - DR Mani
- From the ‡Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | | | | | | | | | - Ruedi Aebersold
- ¶¶Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | | | | | | | - Emily Boja
- National Cancer Institute, NIH Bethesda, Maryland
| | | | | | | | | | - Daniel Chan
- Johns Hopkins University, Baltimore, Maryland
| | - Hasmik Keshishian
- From the ‡Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Eric Kuhn
- From the ‡Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Jerry S.H. Lee
- National Cancer Institute, NIH Bethesda, Maryland
- Johns Hopkins University, Baltimore, Maryland
| | | | - Robert Moritz
- **Institute for Systems Biology, Seattle, Washington
| | | | | | | | | | | | | | | | - Gordon Whiteley
- Liedos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research
| | - Arun Wiita
- ‖‖University of California San Francisco, California
| | - Susan Weintraub
- University of Texas Health Science Center, San Antonio, Texas
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26
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Ramakrishnan R, Tyurin VA, Tuyrin VA, Veglia F, Condamine T, Amoscato A, Mohammadyani D, Johnson JJ, Zhang LM, Klein-Seetharaman J, Celis E, Kagan VE, Gabrilovich DI. Oxidized lipids block antigen cross-presentation by dendritic cells in cancer. THE JOURNAL OF IMMUNOLOGY 2014; 192:2920-31. [PMID: 24554775 DOI: 10.4049/jimmunol.1302801] [Citation(s) in RCA: 192] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Cross-presentation is one of the main features of dendritic cells (DCs), which is critically important for the development of spontaneous and therapy-inducible antitumor immune responses. Patients, at early stages of cancer, have normal presence of DCs. However, the difficulties in the development of antitumor responses in patients with low tumor burden raised the question of the mechanisms of DC dysfunction. In this study, we found that, in differentiated DCs, tumor-derived factors blocked the cross-presentation of exogenous Ags without inhibiting the Ag presentation of endogenous protein or peptides. This effect was caused by intracellular accumulation of different types of oxidized neutral lipids: triglycerides, cholesterol esters, and fatty acids. In contrast, the accumulation of nonoxidized lipids did not affect cross-presentation. Oxidized lipids blocked cross-presentation by reducing the expression of peptide-MHC class I complexes on the cell surface. Thus, this study suggests the novel role of oxidized lipids in the regulation of cross-presentation.
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Affiliation(s)
- Rupal Ramakrishnan
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612
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27
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Chambers AG, Percy AJ, Simon R, Borchers CH. MRM for the verification of cancer biomarker proteins: recent applications to human plasma and serum. Expert Rev Proteomics 2014; 11:137-48. [PMID: 24476379 DOI: 10.1586/14789450.2014.877346] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Accurate cancer biomarkers are needed for early detection, disease classification, prediction of therapeutic response and monitoring treatment. While there appears to be no shortage of candidate biomarker proteins, a major bottleneck in the biomarker pipeline continues to be their verification by enzyme linked immunosorbent assays. Multiple reaction monitoring (MRM), also known as selected reaction monitoring, is a targeted mass spectrometry approach to protein quantitation and is emerging to bridge the gap between biomarker discovery and clinical validation. Highly multiplexed MRM assays are readily configured and enable simultaneous verification of large numbers of candidates facilitating the development of biomarker panels which can increase specificity. This review focuses on recent applications of MRM to the analysis of plasma and serum from cancer patients for biomarker verification. The current status of this approach is discussed along with future directions for targeted mass spectrometry in clinical biomarker validation.
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Affiliation(s)
- Andrew G Chambers
- University of Victoria - Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101 - 4464 Markham St, Victoria, BC V8Z 7X8, Canada
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28
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Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins. Nat Methods 2013; 11:149-55. [PMID: 24317253 PMCID: PMC3922286 DOI: 10.1038/nmeth.2763] [Citation(s) in RCA: 150] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 10/15/2013] [Indexed: 02/07/2023]
Abstract
Multiple reaction monitoring (MRM) mass spectrometry has been successfully applied to monitor targeted proteins in biological specimens, raising the possibility that assays could be configured to measure all human proteins. We report the results of a pilot study designed to test the feasibility of a large-scale, international effort for MRM assay generation. We have configured, validated across three laboratories and made publicly available as a resource to the community 645 novel MRM assays representing 319 proteins expressed in human breast cancer. Assays were multiplexed in groups of >150 peptides and deployed to quantify endogenous analytes in a panel of breast cancer-related cell lines. The median assay precision was 5.4%, with high interlaboratory correlation (R(2) > 0.96). Peptide measurements in breast cancer cell lines were able to discriminate among molecular subtypes and identify genome-driven changes in the cancer proteome. These results establish the feasibility of a large-scale effort to develop an MRM assay resource.
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29
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Vlahou A. Network views for personalized medicine. Proteomics Clin Appl 2013; 7:384-7. [PMID: 23532915 DOI: 10.1002/prca.201200121] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 02/22/2013] [Accepted: 02/25/2013] [Indexed: 11/10/2022]
Abstract
Clinical Proteomics has traveled a long way pinpointing potential biomarkers for a variety of diseases. However, the absence of clinical implementation of proteomics findings has led to a frank evaluation and reconsideration of applied practices in biomarker discovery, recruitment of technological tools for biomarker verification and generation of new guidelines for data reporting. Nevertheless, considering the need for vast clinical resources for biomarker validation, the frequent lack of clear definitions of contexts of use, in combination to the biomarker "high offer," progress toward biomarker implementation will even more require the adoption of an extensive open-minded approach: disease-focused networks are needed to ensure rapid exchange of information, initiation of appropriate studies, parallel validation of multiple biomarkers and sharing of valuable clinical resources. This viewpoint article targets to reflect on these issues and advocates the added value of multidisciplinary networks in biomarker development using bladder cancer as a paradigm.
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Affiliation(s)
- Antonia Vlahou
- Division of Biotechnology, Biomedical Research Foundation, Academy of Athens, 15527 Athens, Greece.
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30
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Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry. Nat Methods 2013; 10:28-34. [PMID: 23269374 DOI: 10.1038/nmeth.2309] [Citation(s) in RCA: 354] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 12/03/2012] [Indexed: 02/06/2023]
Abstract
Targeted mass spectrometry (MS) is becoming widely used in academia and in pharmaceutical and biotechnology industries for sensitive and quantitative detection of proteins, peptides and post-translational modifications. Here we describe the increasing importance of targeted MS technologies in clinical proteomics and the potential key roles these techniques will have in bridging biomedical discovery and clinical implementation.
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31
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Haarberg HE, Paraiso KHT, Wood E, Rebecca VW, Sondak VK, Koomen JM, Smalley KSM. Inhibition of Wee1, AKT, and CDK4 underlies the efficacy of the HSP90 inhibitor XL888 in an in vivo model of NRAS-mutant melanoma. Mol Cancer Ther 2013; 12:901-12. [PMID: 23538902 DOI: 10.1158/1535-7163.mct-12-1003] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The HSP90 inhibitor XL888 is effective at reversing BRAF inhibitor resistance in melanoma, including that mediated through acquired NRAS mutations. The present study has investigated the mechanism of action of XL888 in NRAS-mutant melanoma. Treatment of NRAS-mutant melanoma cell lines with XL888 led to an inhibition of growth, G2-M phase cell-cycle arrest, and the inhibition of cell survival in three-dimensional spheroid and colony formation assays. In vitro, HSP90 inhibition led to the degradation of ARAF, CRAF, Wee1, Chk1, and cdc2 and was associated with decreased mitogen-activated protein kinase (MAPK), AKT, mTOR, and c-jun NH2 kinase (JNK) signaling. Apoptosis induction was associated with increased BIM expression and a decrease in the expression of the prosurvival protein Mcl-1. The critical role of increased BIM and decreased Mcl-1 expression in the survival of NRAS-mutant melanoma cell lines was shown through siRNA knockdown and overexpression studies. In an animal xenograft model of NRAS-mutant melanoma, XL888 treatment led to reduced tumor growth and apoptosis induction. Important differences in the pattern of client degradation were noted between the in vivo and in vitro studies. In vivo, XL888 treatment led to degradation of CDK4 and Wee1 and the inhibition of AKT/S6 signaling with little or no effect observed upon ARAF, CRAF, or MAPK. Blockade of Wee1, using either siRNA knockdown or the inhibitor MK1775, was associated with significant levels of growth inhibition and apoptosis induction. Together, these studies have identified Wee1 as a key target of XL888, suggesting novel therapeutic strategies for NRAS-mutant melanoma.
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Affiliation(s)
- H Eirik Haarberg
- Department of Molecular Oncology, The Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
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32
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Body fluid identification by mass spectrometry. Int J Legal Med 2013; 127:1065-77. [DOI: 10.1007/s00414-013-0848-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 03/05/2013] [Indexed: 12/26/2022]
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33
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Mischak H, Ioannidis JPA, Argiles A, Attwood TK, Bongcam-Rudloff E, Broenstrup M, Charonis A, Chrousos GP, Delles C, Dominiczak A, Dylag T, Ehrich J, Egido J, Findeisen P, Jankowski J, Johnson RW, Julien BA, Lankisch T, Leung HY, Maahs D, Magni F, Manns MP, Manolis E, Mayer G, Navis G, Novak J, Ortiz A, Persson F, Peter K, Riese HH, Rossing P, Sattar N, Spasovski G, Thongboonkerd V, Vanholder R, Schanstra JP, Vlahou A. Implementation of proteomic biomarkers: making it work. Eur J Clin Invest 2012; 42:1027-36. [PMID: 22519700 PMCID: PMC3464367 DOI: 10.1111/j.1365-2362.2012.02674.x] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
While large numbers of proteomic biomarkers have been described, they are generally not implemented in medical practice. We have investigated the reasons for this shortcoming, focusing on hurdles downstream of biomarker verification, and describe major obstacles and possible solutions to ease valid biomarker implementation. Some of the problems lie in suboptimal biomarker discovery and validation, especially lack of validated platforms with well-described performance characteristics to support biomarker qualification. These issues have been acknowledged and are being addressed, raising the hope that valid biomarkers may start accumulating in the foreseeable future. However, successful biomarker discovery and qualification alone does not suffice for successful implementation. Additional challenges include, among others, limited access to appropriate specimens and insufficient funding, the need to validate new biomarker utility in interventional trials, and large communication gaps between the parties involved in implementation. To address this problem, we propose an implementation roadmap. The implementation effort needs to involve a wide variety of stakeholders (clinicians, statisticians, health economists, and representatives of patient groups, health insurance, pharmaceutical companies, biobanks, and regulatory agencies). Knowledgeable panels with adequate representation of all these stakeholders may facilitate biomarker evaluation and guide implementation for the specific context of use. This approach may avoid unwarranted delays or failure to implement potentially useful biomarkers, and may expedite meaningful contributions of the biomarker community to healthcare.
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Affiliation(s)
- Harald Mischak
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
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34
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Boja ES, Rodriguez H. Mass spectrometry-based targeted quantitative proteomics: achieving sensitive and reproducible detection of proteins. Proteomics 2012; 12:1093-110. [PMID: 22577011 DOI: 10.1002/pmic.201100387] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Traditional shotgun proteomics used to detect a mixture of hundreds to thousands of proteins through mass spectrometric analysis, has been the standard approach in research to profile protein content in a biological sample which could lead to the discovery of new (and all) protein candidates with diagnostic, prognostic, and therapeutic values. In practice, this approach requires significant resources and time, and does not necessarily represent the goal of the researcher who would rather study a subset of such discovered proteins (including their variations or posttranslational modifications) under different biological conditions. In this context, targeted proteomics is playing an increasingly important role in the accurate measurement of protein targets in biological samples in the hope of elucidating the molecular mechanism of cellular function via the understanding of intricate protein networks and pathways. One such (targeted) approach, selected reaction monitoring (or multiple reaction monitoring) mass spectrometry (MRM-MS), offers the capability of measuring multiple proteins with higher sensitivity and throughput than shotgun proteomics. Developing and validating MRM-MS-based assays, however, is an extensive and iterative process, requiring a coordinated and collaborative effort by the scientific community through the sharing of publicly accessible data and datasets, bioinformatic tools, standard operating procedures, and well characterized reagents.
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Affiliation(s)
- Emily S Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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35
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Cho WCS. [Proteome profiling for the identification of lung cancer signatures]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2012; 15:C4-7. [PMID: 23676999 PMCID: PMC6134411 DOI: 10.3779/j.issn.1009-3419.2012.07.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
在新近蛋白质组学的发展中,对疾病蛋白质组的综合和深入研究已成为重要议题。已有研究报道了在包括肺癌在内的不同疾病中发现的一些生物标志物,有一些在肺癌诊断和预测中有潜在价值。然而,它们很少作为器官特异性生物标志物以充分比较不同肿瘤类别的模型。本文评价了最近发表的一项在不同基因工程小鼠模型中进行比较蛋白质组的研究,并阐明已发现标志物在人肺癌诊断中的有效性及应用。
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Affiliation(s)
- William C S Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong.
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36
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Domanski D, Cohen Freue GV, Sojo L, Kuzyk MA, Ratkay L, Parker CE, Goldberg YP, Borchers CH. The use of multiplexed MRM for the discovery of biomarkers to differentiate iron-deficiency anemia from anemia of inflammation. J Proteomics 2012; 75:3514-28. [DOI: 10.1016/j.jprot.2011.11.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 11/18/2011] [Indexed: 10/15/2022]
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37
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Cho WCS. Proteome profiling for the identification of lung cancer signatures. Expert Rev Proteomics 2012; 8:689-92. [PMID: 22087654 DOI: 10.1586/epr.11.65] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Comprehensive and in-depth discovery of the disease proteome is an important issue in recent proteomics developments. Previous studies have shown a number of biomarkers discovered in various diseases, including lung cancer. Some of them are potentially useful in lung cancer diagnostics and prognostics. However, few of them can act as organ-specific biomarkers to extensively compare multiple cancer models. This article evaluates a recently published study employing comparative proteomics on multiple genetically engineered mouse models and sheds light on the usefulness and application of the discovered marker panel for human lung cancer diagnostics.
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Affiliation(s)
- William C S Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Room 1305, 13/F, Block R, 30 Gascoigne Road, Kowloon, Hong Kong.
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38
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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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39
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Paraiso KHT, Haarberg HE, Wood E, Rebecca VW, Chen YA, Xiang Y, Ribas A, Lo RS, Weber JS, Sondak VK, John JK, Sarnaik AA, Koomen JM, Smalley KSM. The HSP90 inhibitor XL888 overcomes BRAF inhibitor resistance mediated through diverse mechanisms. Clin Cancer Res 2012; 18:2502-14. [PMID: 22351686 DOI: 10.1158/1078-0432.ccr-11-2612] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
PURPOSE The clinical use of BRAF inhibitors is being hampered by the acquisition of drug resistance. This study shows the potential therapeutic use of the HSP90 inhibitor (XL888) in six different models of vemurafenib resistance. EXPERIMENTAL DESIGN The ability of XL888 to inhibit growth and to induce apoptosis and tumor regression of vemurafenib-resistant melanoma cell lines was shown in vitro and in vivo. A novel mass spectrometry-based pharmacodynamic assay was developed to measure intratumoral HSP70 levels following HSP90 inhibition in melanoma cell lines, xenografts, and melanoma biopsies. Mechanistic studies were carried out to determine the mechanism of XL888-induced apoptosis. RESULTS XL888 potently inhibited cell growth, induced apoptosis, and prevented the growth of vemurafenib-resistant melanoma cell lines in 3-dimensional cell culture, long-term colony formation assays, and human melanoma mouse xenografts. The reversal of the resistance phenotype was associated with the degradation of PDGFRβ, COT, IGFR1, CRAF, ARAF, S6, cyclin D1, and AKT, which in turn led to the nuclear accumulation of FOXO3a, an increase in BIM (Bcl-2 interacting mediator of cell death) expression, and the downregulation of Mcl-1. In most resistance models, XL888 treatment increased BIM expression, decreased Mcl-1 expression, and induced apoptosis more effectively than dual mitogen-activated protein-extracellular signal-regulated kinase/phosphoinositide 3-kinase (MEK/PI3K) inhibition. CONCLUSIONS HSP90 inhibition may be a highly effective strategy at managing the diverse array of resistance mechanisms being reported to BRAF inhibitors and appears to be more effective at restoring BIM expression and downregulating Mcl-1 expression than combined MEK/PI3K inhibitor therapy.
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Affiliation(s)
- Kim H T Paraiso
- The Department of Molecular Oncology, The Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
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40
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Remily-Wood ER, Koomen JM. Evaluation of protein quantification using standard peptides containing single conservative amino acid replacements. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:188-194. [PMID: 22359328 PMCID: PMC3465614 DOI: 10.1002/jms.2053] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Structural analogs are evaluated as peptide internal standards for protein quantification with liquid chromatography-multiple reaction monitoring mass spectrometry (LC-MRM); specifically, single conservative amino acid replacements (SCAR) are performed to create tagged standards that differ by the addition or subtraction of a single methylene group in one amino acid side chain. Because the performance of stable isotope-labeled standards (SIS) has been shown to be superior to structural analogs, differences in both development and quantitative performance between assays based on SIS and SCAR peptides are explored. To establish an assay using the structural analogs, analysis of endogenous, SCAR and SIS peptides was performed to examine their ion signal, fragmentation patterns and response in LC-MRM. Performance of SCAR and SIS peptides was compared for quantification of epidermal growth factor receptor from lung cancer cell lysates and immunoglobulin M in the serum of multiple myeloma patients.
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41
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Xiang Y, Koomen JM. Evaluation of direct infusion-multiple reaction monitoring mass spectrometry for quantification of heat shock proteins. Anal Chem 2012; 84:1981-6. [PMID: 22293045 DOI: 10.1021/ac203011j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein quantification with liquid chromatography-multiple reaction monitoring mass spectrometry (LC-MRM) has emerged as a powerful platform for assessing panels of biomarkers. In this study, direct infusion, using automated, chip-based nanoelectrospray ionization, coupled with MRM (DI-MRM) is used for protein quantification. Removal of the LC separation step increases the importance of evaluating the ratios between the transitions. Therefore, the effects of solvent composition, analyte concentration, spray voltage, and quadrupole resolution settings on fragmentation patterns have been studied using peptide and protein standards. After DI-MRM quantification was evaluated for standards, quantitative assays for the expression of heat shock proteins (HSPs) were translated from LC-MRM to DI-MRM for implementation in cell line models of multiple myeloma. Requirements for DI-MRM assay development are described. Then, the two methods are compared; criteria for effective DI-MRM analysis are reported on the basis of the analysis of HSP expression in digests of whole cell lysates. The increased throughput of DI-MRM analysis is useful for rapid analysis of large batches of similar samples, such as time course measurements of cellular responses to therapy.
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Affiliation(s)
- Yun Xiang
- Molecular Oncology, Moffitt Cancer Center at the University of South Florida, Tampa, Florida 33612, USA
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Parker CE, Domanski D, Percy AJ, Chambers AG, Camenzind AG, Smith DS, Borchers CH. Mass spectrometry in high-throughput clinical biomarker assays: multiple reaction monitoring. Top Curr Chem (Cham) 2012; 336:117-37. [PMID: 22886709 DOI: 10.1007/128_2012_353] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Clinical biomarker discovery, verification, and validation are facilitated by the latest technological advances in mass spectrometry. It is now possible to analyze simultaneously group of tens or hundreds of biomarkers in a blood sample using multiple reaction monitoring (MRM), a tandem mass spectrometric method. However, these newly-developed methods face new challenges, including standardization, calibration, and the determination of analytical and biological variation. Here we illustrate the background, pre-analytical sample preparation, and biomarker assay development using an MRM-mass spectrometric method. In addition, special attention is given to future standardization methods to enable widespread use of the technology.
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Affiliation(s)
- Carol E Parker
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, #3101-4464 Markham Street, Vancouver Island Technology Park, Victoria, BC, V8Z 7X8, Canada
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Hartson SD, Matts RL. Approaches for defining the Hsp90-dependent proteome. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2011; 1823:656-67. [PMID: 21906632 DOI: 10.1016/j.bbamcr.2011.08.013] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 08/22/2011] [Accepted: 08/23/2011] [Indexed: 10/17/2022]
Abstract
Hsp90 is the target of ongoing drug discovery studies seeking new compounds to treat cancer, neurodegenerative diseases, and protein folding disorders. To better understand Hsp90's roles in cellular pathologies and in normal cells, numerous studies have utilized proteomics assays and related high-throughput tools to characterize its physical and functional protein partnerships. This review surveys these studies, and summarizes the strengths and limitations of the individual attacks. We also include downloadable spreadsheets compiling all of the Hsp90-interacting proteins identified in more than 23 studies. These tools include cross-references among gene aliases, human homologues of yeast Hsp90-interacting proteins, hyperlinks to database entries, summaries of canonical pathways that are enriched in the Hsp90 interactome, and additional bioinformatic annotations. In addition to summarizing Hsp90 proteomics studies performed to date and the insights they have provided, we identify gaps in our current understanding of Hsp90-mediated proteostasis. This article is part of a Special Issue entitled: Heat Shock Protein 90 (HSP90).
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Affiliation(s)
- Steven D Hartson
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, USA
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Xiang Y, Remily-Wood ER, Oliveira V, Yarde D, He L, Cheng JQ, Mathews L, Boucher K, Cubitt C, Perez L, Gauthier TJ, Eschrich SA, Shain KH, Dalton WS, Hazlehurst L, Koomen JM. Monitoring a nuclear factor-κB signature of drug resistance in multiple myeloma. Mol Cell Proteomics 2011; 10:M110.005520. [PMID: 21846842 DOI: 10.1074/mcp.m110.005520] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The emergence of acquired drug resistance results from multiple compensatory mechanisms acting to prevent cell death. Simultaneous monitoring of proteins involved in drug resistance is a major challenge for both elucidation of the underlying biology and development of candidate biomarkers for assessment of personalized cancer therapy. Here, we have utilized an integrated analytical platform based on SDS-PAGE protein fractionation prior to liquid chromatography coupled to multiple reaction monitoring mass spectrometry, a versatile and powerful tool for targeted quantification of proteins in complex matrices, to evaluate a well-characterized model system of melphalan resistance in multiple myeloma (MM). Quantitative assays were developed to measure protein expression related to signaling events and biological processes relevant to melphalan resistance in multiple myeloma, specifically: nuclear factor-κB subunits, members of the Bcl-2 family of apoptosis-regulating proteins, and Fanconi Anemia DNA repair components. SDS-PAGE protein fractionation prior to liquid chromatography coupled to multiple reaction monitoring methods were developed for quantification of these selected target proteins in amounts of material compatible with direct translation to clinical specimens (i.e. less than 50,000 cells). As proof of principle, both relative and absolute quantification were performed on cell line models of MM to compare protein expression before and after drug treatment in naïve cells and in drug resistant cells; these liquid chromatography-multiple reaction monitoring results are compared with existing literature and Western blots. The initial stage of a systems biology platform for examining drug resistance in MM has been implemented in cell line models and has been translated to MM cells isolated from a patient. The ultimate application of this platform could assist in clinical decision-making for individualized patient treatment. Although these specific assays have been developed to monitor MM, these techniques are expected to have broad applicability in cancer and other types of disease.
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Affiliation(s)
- Yun Xiang
- Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute University of South Florida, Tampa, FL 33612, USA
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