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Yoon C, Song H, Yin T, Bausch-Fluck D, Frei AP, Kattman S, Dubois N, Witty AD, Hewel JA, Guo H, Emili A, Wollscheid B, Keller G, Zandstra PW. FZD4 Marks Lateral Plate Mesoderm and Signals with NORRIN to Increase Cardiomyocyte Induction from Pluripotent Stem Cell-Derived Cardiac Progenitors. Stem Cell Reports 2017; 10:87-100. [PMID: 29249665 PMCID: PMC5768897 DOI: 10.1016/j.stemcr.2017.11.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 11/13/2017] [Accepted: 11/14/2017] [Indexed: 01/14/2023] Open
Abstract
The identification of cell surface proteins on stem cells or stem cell derivatives is a key strategy for the functional characterization, isolation, and understanding of stem cell population dynamics. Here, using an integrated mass spectrometry- and microarray-based approach, we analyzed the surface proteome and transcriptome of cardiac progenitor cells (CPCs) generated from the stage-specific differentiation of mouse and human pluripotent stem cells. Through bioinformatics analysis, we have identified and characterized FZD4 as a marker for lateral plate mesoderm. Additionally, we utilized FZD4, in conjunction with FLK1 and PDGFRA, to further purify CPCs and increase cardiomyocyte (CM) enrichment in both mouse and human systems. Moreover, we have shown that NORRIN presented to FZD4 further increases CM output via proliferation through the canonical WNT pathway. Taken together, these findings demonstrate a role for FZD4 in mammalian cardiac development. Identified and characterized FZD4 as a new marker for lateral plate mesoderm FZD4, in conjunction with FLK1 and PDGFRA, increases cardiomyocyte enrichment FZD4 is expressed in the human system and shows enrichment in cardiomyocytes NORRIN addition shows increase in cardiomyocyte output from FZD4 progenitor cells
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Affiliation(s)
- Charles Yoon
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - Hannah Song
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - Ting Yin
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - Damaris Bausch-Fluck
- Institute of Molecular Systems Biology at the Department of Health Sciences and Technology, Zurich 8092, Switzerland
| | - Andreas P Frei
- Institute of Molecular Systems Biology at the Department of Health Sciences and Technology, Zurich 8092, Switzerland
| | - Steven Kattman
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada
| | - Nicole Dubois
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada
| | - Alec D Witty
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada
| | - Johannes A Hewel
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Hongbo Guo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Andrew Emili
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Bernd Wollscheid
- Institute of Molecular Systems Biology at the Department of Health Sciences and Technology, Zurich 8092, Switzerland
| | - Gordon Keller
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada
| | - Peter W Zandstra
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Centre for Commercialization of Regenerative Medicine, Toronto, ON M5G 1M1, Canada; Medicine by Design: A Canada First Research Excellence Fund Program, University of Toronto, Toronto, ON M5G 1M1, Canada.
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Hewel JA, Phanse S, Liu J, Bousette N, Gramolini A, Emili A. Targeted protein identification, quantification and reporting for high-resolution nanoflow targeted peptide monitoring. J Proteomics 2012; 81:159-72. [PMID: 23124093 DOI: 10.1016/j.jprot.2012.10.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 10/16/2012] [Accepted: 10/20/2012] [Indexed: 01/29/2023]
Abstract
Mass spectrometry-based targeted proteomic assays are experiencing a surge in awareness due to the diverse possibilities arising from the re-application of traditional LC-SRM technology. The FDA-approved quantitative LC-SRM-pipeline in drug discovery motivates the use to quantitatively validate putative proteomic biomarkers. However, complexity of biological specimens bears a huge challenge to identify, in parallel, specific peptides and proteins of interest from large biomarker candidate lists. Methods have been devised to increase scan speeds, improve detection specificity and verify quantitative SRM-features. In contrast, high-resolution mass spectrometers could be used to improve reliability and precision of targeted proteomics assays. Here, we present a new method for identifying, quantifying and reporting peptides in high-resolution targeted proteomics experiments performed on an orbitrap hybrid instrument using stable isotope-labeled internal reference peptides. This high precision targeted peptide monitoring (TPM) method has unique advantages over existing techniques, including the need to only detect the most abundant product ion of a given target for confident peptide identification using a scoring function that evaluates assay performance based on 1) m/z-mass accuracy, 2) retention time accuracy of observed species relative to prediction, and 3) retention time accuracy relative to internal reference peptides. Further, we show management of multiplexed precision TPM-assays using sentinel peptide standards. This article is part of a Special Issue entitled: From protein structures to clinical applications.
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Affiliation(s)
- Johannes A Hewel
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada.
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Chan JNY, Vuckovic D, Sleno L, Olsen JB, Pogoutse O, Havugimana P, Hewel JA, Bajaj N, Wang Y, Musteata MF, Nislow C, Emili A. Target identification by chromatographic co-elution: monitoring of drug-protein interactions without immobilization or chemical derivatization. Mol Cell Proteomics 2012; 11:M111.016642. [PMID: 22357554 DOI: 10.1074/mcp.m111.016642] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Bioactive molecules typically mediate their biological effects through direct physical association with one or more cellular proteins. The detection of drug-target interactions is therefore essential for the characterization of compound mechanism of action and off-target effects, but generic label-free approaches for detecting binding events in biological mixtures have remained elusive. Here, we report a method termed target identification by chromatographic co-elution (TICC) for routinely monitoring the interaction of drugs with cellular proteins under nearly physiological conditions in vitro based on simple liquid chromatographic separations of cell-free lysates. Correlative proteomic analysis of drug-bound protein fractions by shotgun sequencing is then performed to identify candidate target(s). The method is highly reproducible, does not require immobilization or derivatization of drug or protein, and is applicable to diverse natural products and synthetic compounds. The capability of TICC to detect known drug-protein target physical interactions (K(d) range: micromolar to nanomolar) is demonstrated both qualitatively and quantitatively. We subsequently used TICC to uncover the sterol biosynthetic enzyme Erg6p as a novel putative anti-fungal target. Furthermore, TICC identified Asc1 and Dak1, a core 40 S ribosomal protein that represses gene expression, and dihydroxyacetone kinase involved in stress adaptation, respectively, as novel yeast targets of a dopamine receptor agonist.
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Affiliation(s)
- Janet N Y Chan
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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Brown RB, Hewel JA, Emili A, Audet J. Identification of enzyme-converted peptide products from single cells using capillary electrophoresis and liquid chromatography-mass spectrometry. Methods Mol Biol 2012; 853:17-28. [PMID: 22323137 DOI: 10.1007/978-1-61779-567-1_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Single-cell analysis using chemical methods, otherwise known as chemical cytometry, promises to provide significant leaps in understanding signaling processes which result in cellular behavior. Sensitive methods for chemical cytometry such as capillary electrophoresis can detect and quantify multiple targets; however, conclusive identification of detected analytes is required for useful data to be obtained. Here, we demonstrate a method for determining the identity of enzyme-converted peptide products from single cells using a combination of capillary electrophoresis and liquid chromatography-mass spectrometry (LC-MS).
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Affiliation(s)
- Robert B Brown
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, ON, Canada
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Hewel JA, Liu J, Onishi K, Fong V, Chandran S, Olsen JB, Pogoutse O, Schutkowski M, Wenschuh H, Winkler DFH, Eckler L, Zandstra PW, Emili A. Synthetic peptide arrays for pathway-level protein monitoring by liquid chromatography-tandem mass spectrometry. Mol Cell Proteomics 2010; 9:2460-73. [PMID: 20467045 DOI: 10.1074/mcp.m900456-mcp200] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Effective methods to detect and quantify functionally linked regulatory proteins in complex biological samples are essential for investigating mammalian signaling pathways. Traditional immunoassays depend on proprietary reagents that are difficult to generate and multiplex, whereas global proteomic profiling can be tedious and can miss low abundance proteins. Here, we report a target-driven liquid chromatography-tandem mass spectrometry (LC-MS/MS) strategy for selectively examining the levels of multiple low abundance components of signaling pathways which are refractory to standard shotgun screening procedures and hence appear limited in current MS/MS repositories. Our stepwise approach consists of: (i) synthesizing microscale peptide arrays, including heavy isotope-labeled internal standards, for use as high quality references to (ii) build empirically validated high density LC-MS/MS detection assays with a retention time scheduling system that can be used to (iii) identify and quantify endogenous low abundance protein targets in complex biological mixtures with high accuracy by correlation to a spectral database using new software tools. The method offers a flexible, rapid, and cost-effective means for routine proteomic exploration of biological systems including "label-free" quantification, while minimizing spurious interferences. As proof-of-concept, we have examined the abundance of transcription factors and protein kinases mediating pluripotency and self-renewal in embryonic stem cell populations.
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Affiliation(s)
- Johannes A Hewel
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
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Brown RB, Hewel JA, Emili A, Audet J. Single amino acid resolution of proteolytic fragments generated in individual cells. Cytometry A 2010; 77:347-55. [DOI: 10.1002/cyto.a.20880] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Mak AB, Ni Z, Hewel JA, Chen GI, Zhong G, Karamboulas K, Blakely K, Smiley S, Marcon E, Roudeva D, Li J, Olsen JB, Wan C, Punna T, Isserlin R, Chetyrkin S, Gingras AC, Emili A, Greenblatt J, Moffat J. A lentiviral functional proteomics approach identifies chromatin remodeling complexes important for the induction of pluripotency. Mol Cell Proteomics 2010; 9:811-23. [PMID: 20305087 DOI: 10.1074/mcp.m000002-mcp201] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein complexes and protein-protein interactions are essential for almost all cellular processes. Here, we establish a mammalian affinity purification and lentiviral expression (MAPLE) system for characterizing the subunit compositions of protein complexes. The system is flexible (i.e. multiple N- and C-terminal tags and multiple promoters), is compatible with Gateway cloning, and incorporates a reference peptide. Its major advantage is that it permits efficient and stable delivery of affinity-tagged open reading frames into most mammalian cell types. We benchmarked MAPLE with a number of human protein complexes involved in transcription, including the RNA polymerase II-associated factor, negative elongation factor, positive transcription elongation factor b, SWI/SNF, and mixed lineage leukemia complexes. In addition, MAPLE was used to identify an interaction between the reprogramming factor Klf4 and the Swi/Snf chromatin remodeling complex in mouse embryonic stem cells. We show that the SWI/SNF catalytic subunit Smarca2/Brm is up-regulated during the process of induced pluripotency and demonstrate a role for the catalytic subunits of the SWI/SNF complex during somatic cell reprogramming. Our data suggest that the transcription factor Klf4 facilitates chromatin remodeling during reprogramming.
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Affiliation(s)
- Anthony B Mak
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto M5S3E1, Canada
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Nakorchevsky A, Hewel JA, Kurian SM, Mondala TS, Campbell D, Head SR, Marsh CL, Yates JR, Salomon DR. Molecular mechanisms of chronic kidney transplant rejection via large-scale proteogenomic analysis of tissue biopsies. J Am Soc Nephrol 2010; 21:362-73. [PMID: 20093355 DOI: 10.1681/asn.2009060628] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The most common cause of kidney transplant failure is the poorly characterized histopathologic entity interstitial fibrosis and tubular atrophy (IFTA). There are no known unifying mechanisms, no effective therapy, and no proven preventive strategies. Possible mechanisms include chronic immune rejection, inflammation, drug toxicity, and chronic kidney injury from secondary factors. To gain further mechanistic insight, we conducted a large-scale proteogenomic study of kidney transplant biopsies with IFTA of varying severity. We acquired proteomic data using tandem mass spectrometry with subsequent quantification, analysis of differential protein expression, validation, and functional annotations to known molecular networks. We performed genome-wide expression profiling in parallel. More than 1400 proteins with unique expression profiles traced the progression from normal transplant biopsies to biopsies with mild to moderate and severe disease. Multiple sets of proteins were mapped to different functional pathways, many increasing with histologic severity, including immune responses, inflammatory cell activation, and apoptosis consistent with the chronic rejection hypothesis. Two examples include the extensive population of the alternative rather than the classical complement pathway, previously not appreciated for IFTA, and a comprehensive control network for the actin cytoskeleton and cell signaling of the acute-phase response. In summary, this proteomic effort using kidney tissue contributes mechanistic insight into several biologic processes associated with IFTA.
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Affiliation(s)
- Aleksey Nakorchevsky
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
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Kurian SM, Heilman R, Mondala TS, Nakorchevsky A, Hewel JA, Campbell D, Robison EH, Wang L, Lin W, Gaber L, Solez K, Shidban H, Mendez R, Schaffer RL, Fisher JS, Flechner SM, Head SR, Horvath S, Yates JR, Marsh CL, Salomon DR. Biomarkers for early and late stage chronic allograft nephropathy by proteogenomic profiling of peripheral blood. PLoS One 2009; 4:e6212. [PMID: 19593431 PMCID: PMC2703807 DOI: 10.1371/journal.pone.0006212] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Accepted: 06/04/2009] [Indexed: 12/13/2022] Open
Abstract
Background Despite significant improvements in life expectancy of kidney transplant patients due to advances in surgery and immunosuppression, Chronic Allograft Nephropathy (CAN) remains a daunting problem. A complex network of cellular mechanisms in both graft and peripheral immune compartments complicates the non-invasive diagnosis of CAN, which still requires biopsy histology. This is compounded by non-immunological factors contributing to graft injury. There is a pressing need to identify and validate minimally invasive biomarkers for CAN to serve as early predictors of graft loss and as metrics for managing long-term immunosuppression. Methods We used DNA microarrays, tandem mass spectroscopy proteomics and bioinformatics to identify genomic and proteomic markers of mild and moderate/severe CAN in peripheral blood of two distinct cohorts (n = 77 total) of kidney transplant patients with biopsy-documented histology. Findings Gene expression profiles reveal over 2400 genes for mild CAN, and over 700 for moderate/severe CAN. A consensus analysis reveals 393 (mild) and 63 (moderate/severe) final candidates as CAN markers with predictive accuracy of 80% (mild) and 92% (moderate/severe). Proteomic profiles show over 500 candidates each, for both stages of CAN including 302 proteins unique to mild and 509 unique to moderate/severe CAN. Conclusions This study identifies several unique signatures of transcript and protein biomarkers with high predictive accuracies for mild and moderate/severe CAN, the most common cause of late allograft failure. These biomarkers are the necessary first step to a proteogenomic classification of CAN based on peripheral blood profiling and will be the targets of a prospective clinical validation study.
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Affiliation(s)
- Sunil M. Kurian
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | | | - Tony S. Mondala
- DNA Microarray Core, The Scripps Research Institute, La Jolla, California, United States of America
| | - Aleksey Nakorchevsky
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Johannes A. Hewel
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Daniel Campbell
- DNA Microarray Core, The Scripps Research Institute, La Jolla, California, United States of America
| | - Elizabeth H. Robison
- DNA Microarray Core, The Scripps Research Institute, La Jolla, California, United States of America
| | - Lin Wang
- Department of Biostatistics, University of California, Los Angeles, California, United States of America
| | - Wen Lin
- Department of Biostatistics, University of California, Los Angeles, California, United States of America
| | - Lillian Gaber
- The Texas Medical Center, Houston, Texas, United States of America
| | - Kim Solez
- University of Alberta, Edmonton, Canada
| | - Hamid Shidban
- St. Vincent Medical Center, Los Angeles, California, United States of America
| | - Robert Mendez
- St. Vincent Medical Center, Los Angeles, California, United States of America
| | - Randolph L. Schaffer
- Scripps Center for Organ and Cell Transplantation, Scripps Health, La Jolla, California, United States of America
| | - Jonathan S. Fisher
- Scripps Center for Organ and Cell Transplantation, Scripps Health, La Jolla, California, United States of America
| | - Stuart M. Flechner
- Glickman Urological Institute, The Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Steve R. Head
- DNA Microarray Core, The Scripps Research Institute, La Jolla, California, United States of America
| | - Steve Horvath
- Department of Biostatistics, University of California, Los Angeles, California, United States of America
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Christopher L. Marsh
- Scripps Center for Organ and Cell Transplantation, Scripps Health, La Jolla, California, United States of America
| | - Daniel R. Salomon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
- Scripps Center for Organ and Cell Transplantation, Scripps Health, La Jolla, California, United States of America
- * E-mail:
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Bousette N, Kislinger T, Fong V, Isserlin R, Hewel JA, Emili A, Gramolini AO. Large-Scale Characterization and Analysis of the Murine Cardiac Proteome. J Proteome Res 2009; 8:1887-901. [DOI: 10.1021/pr800845a] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicolas Bousette
- Department of Physiology, University of Toronto, Heart and Stroke/Richard Lewar Centre of Cardiovascular Excellence, Department of Medical Biophysics, University of Toronto, and University Health Network, Toronto, Ontario, Canada, Banting and Best Department of Medical Research, and Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, M5G 1L6, Canada
| | - Thomas Kislinger
- Department of Physiology, University of Toronto, Heart and Stroke/Richard Lewar Centre of Cardiovascular Excellence, Department of Medical Biophysics, University of Toronto, and University Health Network, Toronto, Ontario, Canada, Banting and Best Department of Medical Research, and Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, M5G 1L6, Canada
| | - Vincent Fong
- Department of Physiology, University of Toronto, Heart and Stroke/Richard Lewar Centre of Cardiovascular Excellence, Department of Medical Biophysics, University of Toronto, and University Health Network, Toronto, Ontario, Canada, Banting and Best Department of Medical Research, and Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, M5G 1L6, Canada
| | - Ruth Isserlin
- Department of Physiology, University of Toronto, Heart and Stroke/Richard Lewar Centre of Cardiovascular Excellence, Department of Medical Biophysics, University of Toronto, and University Health Network, Toronto, Ontario, Canada, Banting and Best Department of Medical Research, and Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, M5G 1L6, Canada
| | - Johannes A. Hewel
- Department of Physiology, University of Toronto, Heart and Stroke/Richard Lewar Centre of Cardiovascular Excellence, Department of Medical Biophysics, University of Toronto, and University Health Network, Toronto, Ontario, Canada, Banting and Best Department of Medical Research, and Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, M5G 1L6, Canada
| | - Andrew Emili
- Department of Physiology, University of Toronto, Heart and Stroke/Richard Lewar Centre of Cardiovascular Excellence, Department of Medical Biophysics, University of Toronto, and University Health Network, Toronto, Ontario, Canada, Banting and Best Department of Medical Research, and Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, M5G 1L6, Canada
| | - Anthony O. Gramolini
- Department of Physiology, University of Toronto, Heart and Stroke/Richard Lewar Centre of Cardiovascular Excellence, Department of Medical Biophysics, University of Toronto, and University Health Network, Toronto, Ontario, Canada, Banting and Best Department of Medical Research, and Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, M5G 1L6, Canada
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Hewel JA, Emili A. High-resolution biomarker discovery: Moving from large-scale proteome profiling to quantitative validation of lead candidates. Proteomics Clin Appl 2008; 2:1422-34. [DOI: 10.1002/prca.200800030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Indexed: 12/18/2022]
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12
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Sandhu C, Hewel JA, Badis G, Talukder S, Liu J, Hughes TR, Emili A. Evaluation of Data-Dependent versus Targeted Shotgun Proteomic Approaches for Monitoring Transcription Factor Expression in Breast Cancer. J Proteome Res 2008; 7:1529-41. [DOI: 10.1021/pr700836q] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Charanjit Sandhu
- Program in Proteomics and Bioinformatics, Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research (CCBR), and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Johannes A. Hewel
- Program in Proteomics and Bioinformatics, Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research (CCBR), and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Gwenael Badis
- Program in Proteomics and Bioinformatics, Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research (CCBR), and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Shaheynoor Talukder
- Program in Proteomics and Bioinformatics, Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research (CCBR), and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jian Liu
- Program in Proteomics and Bioinformatics, Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research (CCBR), and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Timothy R. Hughes
- Program in Proteomics and Bioinformatics, Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research (CCBR), and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Andrew Emili
- Program in Proteomics and Bioinformatics, Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research (CCBR), and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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Abstract
Endothelial progenitor cells (EPCs) have significant therapeutic potential. However, the low quantity of such cells available from bone marrow and their limited capacity to proliferate in culture make their use difficult. Here, we present the first definitive demonstration of the presence of true EPCs in murine fetal liver capable of forming blood vessels in vivo connected to the host's vasculature after transplantation. This population is particularly interesting because it can be obtained at high yield and has a high angiogenic capacity as compared with bone marrow-derived EPCs. The EPC capacity is contained within the CD31+Sca1+ cell subset. We demonstrate that these cells are dependent for survival and proliferation on a feeder cell monolayer derived from the fetal liver. In addition, we describe a novel and easy method for the isolation and ex vivo proliferation of these EPCs. Finally, we used gene expression profiling and tandem mass spectrometry proteomics to examine the fetal liver endothelial progenitors and the feeder cells to identify possible proangiogenic growth factor and endothelial differentiation-associated genes.
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Affiliation(s)
- Stephanie Cherqui
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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