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Carbonara K, Padula MP, Coorssen JR. Quantitative assessment confirms deep proteome analysis by integrative top-down proteomics. Electrophoresis 2023; 44:472-480. [PMID: 36416355 DOI: 10.1002/elps.202200257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022]
Abstract
The goal of integrative top-down proteomics (i.e., two-dimensional gel electrophoresis [2DE] coupled with liquid chromatography and tandem mass spectrometry [LC/MS/MS]) is a routine analytical approach that fully addresses the breadth and depth of proteomes. To accomplish this, there should be no addition, removal, or modification to any constituent proteoforms. To address two-decade old claims of protein losses during front-end proteome resolution using 2DE, here we tested an alternate rehydration method for immobilized pH gradient strips prior to isoelectric focusing (IEF; i.e., faceup compared to facedown) and quantitatively assessed losses during the front-end of 2DE (rehydration and IEF). Using a well-established high-resolution, quantitative 2DE protocol, there were no detectable proteoform losses using the alternate faceup rehydration method. Although there is a <0.25% total loss of proteoforms during standard facedown rehydration, it is insignificant in terms of having any effect on overall proteome resolution (i.e., total spot count and total spot signal). This report is another milestone in integrative top-down proteomics, disproving long-held dogma in the field and confirming that quantitative front-end 2DE/LC/MS/MS is currently the only method to broadly and deeply analyze proteomes by resolving their constituent proteoforms.
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Affiliation(s)
- Katrina Carbonara
- Department of Health Sciences, Faculty of Applied Health Sciences, Brock University, St. Catharines, Ontario, Canada
| | - Matthew P Padula
- School of Life Sciences and Proteomics, Lipidomics and Metabolomics Core Facility, Faculty of Science, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Jens R Coorssen
- Department of Biological Sciences, Faculty of Mathematics and Science, Brock University, St. Catharines, Ontario, Canada.,Ronin Institute, Montclair, New Jersey, USA
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2
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Michaud SA, Pětrošová H, Jackson AM, McGuire JC, Sinclair NJ, Ganguly M, Flenniken AM, Nutter LMJ, McKerlie C, Schibli D, Smith D, Borchers CH. Process and Workflow for Preparation of Disparate Mouse Tissues for Proteomic Analysis. J Proteome Res 2020; 20:305-316. [PMID: 33151080 DOI: 10.1021/acs.jproteome.0c00399] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigated the effect of homogenization strategy and protein precipitation on downstream protein quantitation using multiple reaction monitoring mass spectrometry (MRM-MS). Our objective was to develop a workflow capable of processing disparate tissue types with high throughput, minimal variability, and maximum purity. Similar abundances of endogenous proteins were measured in nine different mouse tissues regardless of the homogenization method used; however, protein precipitation had strong positive effects on several targets. The best throughput was achieved by lyophilizing tissues to dryness, followed by homogenization via bead-beating without sample buffer. Finally, the effect of tissue perfusion prior to dissection and collection was explored in 20 mouse tissues. MRM-MS showed decreased abundances of blood-related proteins in perfused tissues; however, complete removal was not achieved. Concentrations of nonblood proteins were largely unchanged, although significantly higher variances were observed for proteins from the perfused lung, indicating that perfusion may not be suitable for this organ. We present a simple yet effective tissue processing workflow consisting of harvest of fresh nonperfused tissue, novel lyophilization and homogenization by bead-beating, and protein precipitation. This workflow can be applied to a range of mouse tissues with the advantages of simplicity, minimal manual manipulation of samples, use of commonly available equipment, and high sample quality.
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Affiliation(s)
- Sarah A Michaud
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria V8Z 7X8, British Columbia, Canada
| | - Helena Pětrošová
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria V8Z 7X8, British Columbia, Canada
| | - Angela M Jackson
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria V8Z 7X8, British Columbia, Canada
| | - Jamie C McGuire
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria V8Z 7X8, British Columbia, Canada
| | - Nicholas J Sinclair
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria V8Z 7X8, British Columbia, Canada
| | - Milan Ganguly
- The Center for Phenogenomics, Toronto M5T 3H7, Ontario, Canada.,The Hospital for Sick Children, Toronto M5G 1X8, Ontario, Canada
| | - Ann M Flenniken
- The Center for Phenogenomics, Toronto M5T 3H7, Ontario, Canada.,Sinai Health Lunenfeld-Tanenbaum Research Institute, Toronto M5G 1X5, Ontario, Canada
| | - Lauryl M J Nutter
- The Center for Phenogenomics, Toronto M5T 3H7, Ontario, Canada.,The Hospital for Sick Children, Toronto M5G 1X8, Ontario, Canada
| | - Colin McKerlie
- The Center for Phenogenomics, Toronto M5T 3H7, Ontario, Canada.,The Hospital for Sick Children, Toronto M5G 1X8, Ontario, Canada
| | - David Schibli
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria V8Z 7X8, British Columbia, Canada
| | - Derek Smith
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria V8Z 7X8, British Columbia, Canada
| | - Christoph H Borchers
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria V8Z 7X8, British Columbia, Canada.,Department of Data Intensive Science and Engineering, Skolkovo Innovation Center, Skolkovo Institute of Science and Technology, Nobel Street, Moscow 143026, Russia.,Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal H3T 1E2, Quebec, Canada.,Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal H3T 1E2, Quebec, Canada
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3
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Kwok CSN, Lai KKY, Lam SW, Chan KK, Xu SJL, Lee FWF. Production of high-quality two-dimensional gel electrophoresis profile for marine medaka samples by using Trizol-based protein extraction approaches. Proteome Sci 2020; 18:5. [PMID: 32390769 PMCID: PMC7196234 DOI: 10.1186/s12953-020-00161-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 04/22/2020] [Indexed: 12/25/2022] Open
Abstract
Background Marine medaka is among the most popular models of fish species for ecotoxicology and environmental research and proteomic studies are useful tools for understanding the molecular responses of medaka upon exposure to different environmental stressors. The preparation of high-quality protein samples is the key to producing high-quality two-dimensional gel electrophoresis (2-DE) results for proteomic analysis. In recent years, Trizol-based protein extraction has been gaining popularity because of its promising performance in producing high-quality 2-DE as well as the convenience of the method. Methods Three Trizol-based approaches (Trizol method, Aliquot Trizol method and Trizol method with a commercial clean-up kit) were used to extract proteins from a marine medaka sample and 2-DE profiles were produced. Quality of the 2-DE profiles and effectiveness of the extraction methods were evaluated. For comparison, two common protein extraction methods (lysis buffer method and trichloroacetic acid (TCA)/acetone precipitation extraction) were also applied in parallel to Trizol-based approaches. Results Any of the three Trizol-based approaches produced a high-quality 2-DE profile of marine medaka compared with both lysis buffer method and TCA/acetone precipitation extraction. In addition, Trizol method with a commercial clean-up kit produced the best 2-DE profile in terms of background clarity, number of spots and resolution of proteins. Conclusions Trizol-based approaches offered better choices than traditional protein extraction methods for 2-DE analysis of marine medaka. The modified version of Trizol method with a commercial clean-up kit was shown to produce the best 2-DE profile.
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Affiliation(s)
- Celia Sze-Nga Kwok
- Department of Science, School of Science and Technology, The Open University of Hong Kong, Hong Kong, SAR China
| | - Kaze King-Yip Lai
- Department of Science, School of Science and Technology, The Open University of Hong Kong, Hong Kong, SAR China
| | - Sai-Wo Lam
- Department of Science, School of Science and Technology, The Open University of Hong Kong, Hong Kong, SAR China
| | - Kin-Ka Chan
- Department of Science, School of Science and Technology, The Open University of Hong Kong, Hong Kong, SAR China
| | - Steven Jing-Liang Xu
- Department of Science, School of Science and Technology, The Open University of Hong Kong, Hong Kong, SAR China
| | - Fred Wang-Fat Lee
- Department of Science, School of Science and Technology, The Open University of Hong Kong, Hong Kong, SAR China
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4
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Suppression of the Peripheral Immune System Limits the Central Immune Response Following Cuprizone-Feeding: Relevance to Modelling Multiple Sclerosis. Cells 2019; 8:cells8111314. [PMID: 31653054 PMCID: PMC6912385 DOI: 10.3390/cells8111314] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/18/2019] [Accepted: 10/18/2019] [Indexed: 02/06/2023] Open
Abstract
Cuprizone (CPZ) preferentially affects oligodendrocytes (OLG), resulting in demyelination. To investigate whether central oligodendrocytosis and gliosis triggered an adaptive immune response, the impact of combining a standard (0.2%) or low (0.1%) dose of ingested CPZ with disruption of the blood brain barrier (BBB), using pertussis toxin (PT), was assessed in mice. 0.2% CPZ(±PT) for 5 weeks produced oligodendrocytosis, demyelination and gliosis plus marked splenic atrophy (37%) and reduced levels of CD4 (44%) and CD8 (61%). Conversely, 0.1% CPZ(±PT) produced a similar oligodendrocytosis, demyelination and gliosis but a smaller reduction in splenic CD4 (11%) and CD8 (14%) levels and no splenic atrophy. Long-term feeding of 0.1% CPZ(±PT) for 12 weeks produced similar reductions in CD4 (27%) and CD8 (43%), as well as splenic atrophy (33%), as seen with 0.2% CPZ(±PT) for 5 weeks. Collectively, these results suggest that 0.1% CPZ for 5 weeks may be a more promising model to study the ‘inside-out’ theory of Multiple Sclerosis (MS). However, neither CD4 nor CD8 were detected in the brain in CPZ±PT groups, indicating that CPZ-mediated suppression of peripheral immune organs is a major impediment to studying the ‘inside-out’ role of the adaptive immune system in this model over long time periods. Notably, CPZ(±PT)-feeding induced changes in the brain proteome related to the suppression of immune function, cellular metabolism, synaptic function and cellular structure/organization, indicating that demyelinating conditions, such as MS, can be initiated in the absence of adaptive immune system involvement.
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5
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Mazinani SA, Noaman N, Pergande MR, Cologna S, Coorssen J, Yan H. Exposure to microwave irradiation at constant culture temperature slows the growth of Escherichia coliDE3 cells, leading to modified proteomic profiles. RSC Adv 2019; 9:11810-11817. [PMID: 35517035 PMCID: PMC9063421 DOI: 10.1039/c9ra00617f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 04/07/2019] [Indexed: 11/21/2022] Open
Abstract
E. coligrowth is slowed by exposure to non-lethal microwave irradiation, accompanied by changes in proteomic profiles.
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Affiliation(s)
- Sina Atrin Mazinani
- Department of Chemistry and Centre for Biotechnology
- Brock University
- Ontario
- Canada
| | - Nour Noaman
- Department of Applied Health Sciences
- Department of Biological Sciences
- Brock University
- Ontario
- Canada
| | | | | | - Jens Coorssen
- Department of Applied Health Sciences
- Department of Biological Sciences
- Brock University
- Ontario
- Canada
| | - Hongbin Yan
- Department of Chemistry and Centre for Biotechnology
- Brock University
- Ontario
- Canada
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6
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Khudyakov JI, Deyarmin JS, Hekman RM, Pujade Busqueta L, Maan R, Mody MJ, Banerjee R, Crocker DE, Champagne CD. A sample preparation workflow for adipose tissue shotgun proteomics and proteogenomics. Biol Open 2018; 7:bio.036731. [PMID: 30361411 PMCID: PMC6262853 DOI: 10.1242/bio.036731] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Animals with large adipose stores, such as marine mammals, may provide insights into the evolution and function of this multifunctional tissue in health and disease. In the absence of sequenced genomes, molecular information can be rapidly obtained by proteomics and transcriptomics, but their application to adipose tissue is hindered by low nucleic acid and protein yields. We sequenced and compared proteomes isolated from the blubber of four elephant seals using phenol and guanidine thiocyanate (Qiazol) or detergent (sodium deoxycholate) buffer. Qiazol recovered more subcellular proteins such as metabolic enzymes, in addition to extracting RNA, facilitating proteogenomic analyses of small lipid-rich tissue biopsies. We also compared proteomics data analysis platforms and found that de novo peptide sequencing improved protein identification sensitivity compared to database search alone. We report sample preparation and data analysis workflows for proteogenomics and a proteome of elephant seal blubber containing 2678 proteins, including many of interest for further functional studies. This article has an associated First Person interview with the first author of the paper. Summary: Proteins that are compatible with shotgun proteomics can be isolated from small amounts of adipose tissue at the same time as RNA, facilitating proteogenomics studies in non-model animals.
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Affiliation(s)
- Jane I Khudyakov
- Department of Biological Sciences, University of the Pacific, Stockton, CA, USA .,Conservation and Biological Research Program, National Marine Mammal Foundation, San Diego, CA, USA
| | - Jared S Deyarmin
- Department of Biological Sciences, University of the Pacific, Stockton, CA, USA
| | - Ryan M Hekman
- Department of Biological Sciences, University of the Pacific, Stockton, CA, USA
| | | | - Rasool Maan
- Department of Biological Sciences, University of the Pacific, Stockton, CA, USA
| | - Melony J Mody
- Department of Biological Sciences, University of the Pacific, Stockton, CA, USA
| | - Reeti Banerjee
- Department of Biological Sciences, University of the Pacific, Stockton, CA, USA
| | - Daniel E Crocker
- Department of Biology, Sonoma State University, Rohnert Park, CA, USA
| | - Cory D Champagne
- Conservation and Biological Research Program, National Marine Mammal Foundation, San Diego, CA, USA
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7
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Abbineni PS, Coorssen JR. Sphingolipids modulate docking, Ca 2+ sensitivity and membrane fusion of native cortical vesicles. Int J Biochem Cell Biol 2018; 104:43-54. [PMID: 30195064 DOI: 10.1016/j.biocel.2018.09.001] [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] [Received: 07/06/2018] [Revised: 08/31/2018] [Accepted: 09/01/2018] [Indexed: 12/16/2022]
Abstract
Docking, priming, and membrane fusion of secretory vesicles (i.e. regulated exocytosis) requires lipids and proteins. Sphingolipids, in particular, sphingosine and sphingosine-1-phosphate, have been implicated in the modulation of exocytosis. However, the specific exocytotic steps that sphingolipids modulate and the enzymes that regulate sphingolipid concentrations on native secretory vesicle membranes remain unknown. Here we use tightly coupled functional and molecular analyses of fusion-ready cell surface complexes and cortical vesicles isolated from oocytes to assess the role of sphingolipids in the late, Ca2+-triggered steps of exocytosis. The molecular changes resulting from treatments with sphingolipid modifying compounds coupled with immunoblotting analysis revealed the presence of sphingosine kinase on native vesicles; the presence of a sphingosine-1-phosphate phosphatase is also indicated. Changes in sphingolipid concentrations on vesicles altered their docking/priming, Ca2+-sensitivity, and ability to fuse, indicating that sphingolipid concentrations are tightly regulated and maintained at optimal levels and ratios to ensure efficient exocytosis.
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Affiliation(s)
- Prabhodh S Abbineni
- Department of Molecular Physiology, and the WSU Molecular Medicine Research Group, School of Medicine, Western Sydney University, Campbelltown, NSW, 2560, Australia
| | - Jens R Coorssen
- Department of Health Sciences, Faculty of Applied Health Sciences, Department of Biology, Faculty of Mathematics and Science, Brock University, St. Catharines, Ontario, Canada.
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8
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Evaluation of the Use of TRIzol-Based Protein Extraction Approach for Gel-Based Proteomic Analysis of Dried Seafood Products and Chinese Tonic Foods. Int J Mol Sci 2018; 19:ijms19071998. [PMID: 29987231 PMCID: PMC6073523 DOI: 10.3390/ijms19071998] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 06/30/2018] [Accepted: 07/06/2018] [Indexed: 12/15/2022] Open
Abstract
Although the emergence of gel-free approaches has greatly enhanced proteomic studies, two-dimensional gel electrophoresis (2-DE) remains one of the most widely used proteomic techniques for its high resolving power, relatively low cost, robustness, and high resolution. Preparation of high-quality protein samples remains the key in high-quality 2-DE for proteomic analysis. Samples with high endogenous levels of interfering molecules, such as salts, nucleic acids, lipids, and polysaccharides, would yield a low-quality 2-DE gel and hinder the analysis. Recently, a TRIzol-based protein extraction method has gained prominence and has attracted attention due to its promising performance in high-quality 2-DE. The authors evaluate the use of this approach for four valuable dried food products, namely two dried seafood products (abalone slices and whelk slices) and two traditional Chinese tonic foods (ganoderma and caterpillar fungus). The results indicate that 2-DE gels obtained through the TRIzol-based method are of high-quality and are comparable to those obtained through the trichloroacetic acid⁻acetone method in terms of spot number, spot intensity, and resolution. The TRIzol-based method is generally applicable to dried food samples and is simple and fast, which greatly streamlines the protein extraction procedure. Additionally, it enables the concurrent extraction and analysis of RNA, DNA, and protein from the same sample.
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9
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Proteomic analysis of first trimester maternal serum to identify candidate biomarkers potentially predictive of spontaneous preterm birth. J Proteomics 2018; 178:31-42. [PMID: 29448056 DOI: 10.1016/j.jprot.2018.02.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 01/29/2018] [Accepted: 02/02/2018] [Indexed: 01/01/2023]
Abstract
Spontaneous preterm birth (sPTB) remains a major clinical dilemma; current diagnostics and interventions have not reduced the rate of this serious healthcare burden. This study characterizes differential protein profiles and post-translational modifications (PTMs) in first trimester maternal serum using a refined top-down approach coupling two-dimensional gel electrophoresis (2DE) and mass spectrometry (MS) to directly compare subsequent term and preterm labour events and identify marked protein differences. 30 proteoforms were found to be significantly increased or decreased in the sPTB group including 9 phosphoproteins and 11 glycoproteins. Changes occurred in proteins associated with immune and defence responses. We identified protein species that are associated with several clinically relevant biological processes, including interrelated biological networks linked to regulation of the complement cascade and coagulation pathways, immune modulation, metabolic processes and cell signalling. The finding of altered proteoforms in maternal serum from pregnancies that delivered preterm suggests these as potential early biomarkers of sPTB and also possible mediators of the disorder. BIOLOGICAL SIGNIFICANCE Identifying changes in protein profiles is critical in the study of cell biology, and disease treatment and prevention. Identifying consistent changes in the maternal serum proteome during early pregnancy, including specific protein PTMs (e.g. phosphorylation, glycosylation), is likely to provide better opportunities for prediction, intervention and prevention of preterm birth. This is the first study to examine first trimester maternal serum using a highly refined top-down proteomic analytical approach based on high resolution 2DE coupled with mass spectrometry to directly compare preterm (<37 weeks) and preterm (≥37 weeks) events and identify select protein differences between these conditions. As such, the data present a promising avenue for translation of biomarker discovery to a clinical setting as well as for future investigation of underlying aetiological processes.
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10
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Noaman N, Abbineni PS, Withers M, Coorssen JR. Coomassie staining provides routine (sub)femtomole in-gel detection of intact proteoforms: Expanding opportunities for genuine Top-down Proteomics. Electrophoresis 2017; 38:3086-3099. [PMID: 28872692 DOI: 10.1002/elps.201700190] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 07/11/2017] [Accepted: 08/25/2017] [Indexed: 01/22/2023]
Abstract
Modified colloidal Coomassie Brilliant Blue (cCBB) staining utilising a novel destain protocol and near-infrared fluorescence detection (nIRFD) rivals the in-gel protein detection sensitivity (DS) of SYPRO Ruby. However, established DS estimates are likely inaccurate in terms of 2DE-resolved proteoform 'spots' since DS is routinely measured from comparatively diffuse protein 'bands' following wide-well 1DE. Here, cCBB DS for 2DE-based proteomics was more accurately determined using narrow-well 1DE. As precise estimates of protein standard monomer concentrations are essential for accurate quantitation, coupling UV absorbance with gel-based purity assessments is described. Further, as cCBB is compatible with both nIRFD and densitometry, the impacts of imaging method (and image resolution) on DS were assessed. Narrow-well 1DE enabled more accurate quantitation of cCBB DS for 2DE, achieving (sub)femtomole DS with either nIRFD or densitometry. While densitometry offers comparative simplicity and affordability, nIRFD has the unique potential for enhanced DS with Deep Imaging. Higher-resolution nIRFD also improved analysis of a 2DE-resolved proteome, surpassing the DS of standard nIRFD and densitometry, with nIRFD Deep Imaging further maximising proteome coverage. cCBB DS for intact proteins rivals that of mass spectrometry (MS) for peptides in complex mixtures, reaffirming that 2DE-MS currently provides the most routine, broadly applicable, robust, and information-rich Top-down approach to Discovery Proteomics.
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Affiliation(s)
- Nour Noaman
- Department of Molecular Physiology, and the WSU Molecular Medicine Research Group, School of Medicine, Western Sydney University, Campbelltown, New South Wales, Australia
| | - Prabhodh S Abbineni
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Michael Withers
- Department of Molecular Physiology, and the WSU Molecular Medicine Research Group, School of Medicine, Western Sydney University, Campbelltown, New South Wales, Australia
| | - Jens R Coorssen
- Departments of Health Sciences and Biological Sciences, Brock University, St Catharines, Ontario, Canada
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A Routine 'Top-Down' Approach to Analysis of the Human Serum Proteome. Proteomes 2017; 5:proteomes5020013. [PMID: 28587287 PMCID: PMC5489773 DOI: 10.3390/proteomes5020013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/30/2017] [Accepted: 05/30/2017] [Indexed: 12/21/2022] Open
Abstract
Serum provides a rich source of potential biomarker proteoforms. One of the major obstacles in analysing serum proteomes is detecting lower abundance proteins owing to the presence of hyper-abundant species (e.g., serum albumin and immunoglobulins). Although depletion methods have been used to address this, these can lead to the concomitant removal of non-targeted protein species, and thus raise issues of specificity, reproducibility, and the capacity for meaningful quantitative analyses. Altering the native stoichiometry of the proteome components may thus yield a more complex series of issues than dealing directly with the inherent complexity of the sample. Hence, here we targeted method refinements so as to ensure optimum resolution of serum proteomes via a top down two-dimensional gel electrophoresis (2DE) approach that enables the routine assessment of proteoforms and is fully compatible with subsequent mass spectrometric analyses. Testing included various fractionation and non-fractionation approaches. The data show that resolving 500 µg protein on 17 cm 3–10 non-linear immobilised pH gradient strips in the first dimension followed by second dimension resolution on 7–20% gradient gels with a combination of lithium dodecyl sulfate (LDS) and sodium dodecyl sulfate (SDS) detergents markedly improves the resolution and detection of proteoforms in serum. In addition, well established third dimension electrophoretic separations in combination with deep imaging further contributed to the best available resolution, detection, and thus quantitative top-down analysis of serum proteomes.
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12
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A Comprehensive Guide for Performing Sample Preparation and Top-Down Protein Analysis. Proteomes 2017; 5:proteomes5020011. [PMID: 28387712 PMCID: PMC5489772 DOI: 10.3390/proteomes5020011] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 04/04/2017] [Accepted: 04/04/2017] [Indexed: 12/21/2022] Open
Abstract
Methodologies for the global analysis of proteins in a sample, or proteome analysis, have been available since 1975 when Patrick O′Farrell published the first paper describing two-dimensional gel electrophoresis (2D-PAGE). This technique allowed the resolution of single protein isoforms, or proteoforms, into single ‘spots’ in a polyacrylamide gel, allowing the quantitation of changes in a proteoform′s abundance to ascertain changes in an organism′s phenotype when conditions change. In pursuit of the comprehensive profiling of the proteome, significant advances in technology have made the identification and quantitation of intact proteoforms from complex mixtures of proteins more routine, allowing analysis of the proteome from the ‘Top-Down’. However, the number of proteoforms detected by Top-Down methodologies such as 2D-PAGE or mass spectrometry has not significantly increased since O’Farrell’s paper when compared to Bottom-Up, peptide-centric techniques. This article explores and explains the numerous methodologies and technologies available to analyse the proteome from the Top-Down with a strong emphasis on the necessity to analyse intact proteoforms as a better indicator of changes in biology and phenotype. We arrive at the conclusion that the complete and comprehensive profiling of an organism′s proteome is still, at present, beyond our reach but the continuing evolution of protein fractionation techniques and mass spectrometry brings comprehensive Top-Down proteome profiling closer.
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13
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Partridge MA, Gopinath S, Myers SJ, Coorssen JR. An initial top-down proteomic analysis of the standard cuprizone mouse model of multiple sclerosis. J Chem Biol 2015; 9:9-18. [PMID: 26855677 DOI: 10.1007/s12154-015-0138-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 05/28/2015] [Indexed: 11/29/2022] Open
Abstract
An initial proteomic analysis of the cuprizone mouse model to characterise the breadth of toxicity by assessing cortex, skeletal muscle, spleen and peripheral blood mononuclear cells. Cuprizone treated vs. control mice for an initial characterisation. Select tissues from each group were pooled, analysed in triplicate using two-dimensional gel electrophoresis (2DE) and deep imaging and altered protein species identified using liquid chromatography tandem mass spectrometry (LC/MS/MS). Forty-three proteins were found to be uniquely detectable or undetectable in the cuprizone treatment group across the tissues analysed. Protein species identified in the cortex may potentially be linked to axonal damage in this model, and those in the spleen and peripheral blood mononuclear cells to the minimal peripheral immune cell infiltration into the central nervous system during cuprizone mediated demyelination. Primary oligodendrocytosis has been observed in type III lesions in multiple sclerosis. However, the underlying mechanisms are poorly understood. Cuprizone treatment results in oligodendrocyte apoptosis and secondary demyelination. This initial analysis identified proteins likely related to axonal damage; these may link primary oligodendrocytosis and secondary axonal damage. Furthermore, this appears to be the first study of the cuprizone model to also identify alterations in the proteomes of skeletal muscle, spleen and peripheral blood mononuclear cells. Notably, protein disulphide isomerase was not detected in the cuprizone cohort; its absence has been linked to reduced major histocompatibility class I assembly and reduced antigen presentation. Overall, the results suggest that, like experimental autoimmune encephalomyelitis, results from the standard cuprizone model should be carefully considered relative to clinical multiple sclerosis.
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Affiliation(s)
- Melissa A Partridge
- Department of Molecular Physiology, School of Medicine, University of Western Sydney, Penrith, NSW Australia ; Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Penrith, NSW Australia
| | - Sumana Gopinath
- Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Penrith, NSW Australia ; Department of Neurology, Campbelltown Hospital, Campbelltown, NSW Australia
| | - Simon J Myers
- Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Penrith, NSW Australia ; Neuro-Cell Biology Laboratory, School of Science and Health, University of Western Sydney, Penrith, NSW Australia
| | - Jens R Coorssen
- Department of Molecular Physiology, School of Medicine, University of Western Sydney, Penrith, NSW Australia ; Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Penrith, NSW Australia
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14
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Stimpson SE, Coorssen JR, Myers SJ. Optimal isolation of mitochondria for proteomic analyses. Anal Biochem 2015; 475:1-3. [DOI: 10.1016/j.ab.2015.01.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/23/2014] [Accepted: 01/08/2015] [Indexed: 12/24/2022]
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15
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Saxena T, Loomis KH, Pai SB, Karumbaiah L, Gaupp E, Patil K, Patkar R, Bellamkonda RV. Nanocarrier-mediated inhibition of macrophage migration inhibitory factor attenuates secondary injury after spinal cord injury. ACS NANO 2015; 9:1492-505. [PMID: 25587936 DOI: 10.1021/nn505980z] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Spinal cord injury (SCI) can lead to permanent motor and sensory deficits. Following the initial traumatic insult, secondary injury mechanisms characterized by persistent heightened inflammation are initiated and lead to continued and pervasive cell death and tissue damage. Anti-inflammatory drugs such as methylprednisolone (MP) used clinically have ambiguous benefits with debilitating side effects. Typically, these drugs are administered systemically at high doses, resulting in toxicity and paradoxically increased inflammation. Furthermore, these drugs have a small time window postinjury (few hours) during which they need to be infused to be effective. As an alternative to MP, we investigated the effect of a small molecule inhibitor (Chicago sky blue, CSB) of macrophage migration inhibitory factor (MIF) for treating SCI. The pleiotropic cytokine MIF is known to contribute to upregulation of several pro-inflammatory cytokines in various disease and injury states. In vitro, CSB administration alleviated endotoxin-mediated inflammation in primary microglia and macrophages. Nanocarriers such as liposomes can potentially alleviate systemic side effects of high-dose therapy by enabling site-specific drug delivery to the spinal cord. However, the therapeutic window of 100 nm scale nanoparticle localization to the spinal cord after contusion injury is not fully known. Thus, we first investigated the ability of nanocarriers of different sizes to localize to the injured spinal cord up to 2 weeks postinjury. Results from the study showed that nanocarriers as large as 200 nm in diameter could extravasate into the injured spinal cord up to 96 h postinjury. We then formulated nanocarriers (liposomes) encapsulating CSB and administered them intravenously 48 h postinjury, within the previously determined 96 h therapeutic window. In vivo, in this clinically relevant contusion injury model in rats, CSB administration led to preservation of vascular and white matter integrity, improved wound healing, and an increase in levels of arginase and other transcripts indicative of a resolution phase of wound healing. This study demonstrates the potential of MIF inhibition in SCI and the utility of nanocarrier-mediated drug delivery selectively to the injured cord.
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Affiliation(s)
- Tarun Saxena
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine , Atlanta, Georgia 30332, United States
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16
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Braakman RBH, Bezstarosti K, Sieuwerts AM, de Weerd V, van Galen AM, Stingl C, Luider TM, Timmermans MAM, Smid M, Martens JWM, Foekens JA, Demmers JAA, Umar A. Integrative Analysis of Genomics and Proteomics Data on Clinical Breast Cancer Tissue Specimens Extracted with Acid Guanidinium Thiocyanate–Phenol–Chloroform. J Proteome Res 2015; 14:1627-36. [DOI: 10.1021/acs.jproteome.5b00046] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- René B. H. Braakman
- Department
of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam,
Be401, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
- Postgraduate
School of Molecular Medicine, Erasmus MC, University Medical Center Rotterdam, Dr Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Karel Bezstarosti
- Proteomics
Center, Erasmus MC, University Medical Center Rotterdam, Dr Molewaterplein
50, 3015 GE Rotterdam, The Netherlands
| | - Anieta M. Sieuwerts
- Department
of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam,
Be401, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
- Postgraduate
School of Molecular Medicine, Erasmus MC, University Medical Center Rotterdam, Dr Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Vanja de Weerd
- Department
of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam,
Be401, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Anne M. van Galen
- Department
of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam,
Be401, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Christoph Stingl
- Department
of Neurology, Erasmus MC, University Medical Center Rotterdam, Dr
Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Theo M. Luider
- Department
of Neurology, Erasmus MC, University Medical Center Rotterdam, Dr
Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Mieke A. M. Timmermans
- Department
of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam,
Be401, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Marcel Smid
- Department
of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam,
Be401, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - John W. M. Martens
- Department
of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam,
Be401, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
- Postgraduate
School of Molecular Medicine, Erasmus MC, University Medical Center Rotterdam, Dr Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - John A. Foekens
- Department
of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam,
Be401, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
- Postgraduate
School of Molecular Medicine, Erasmus MC, University Medical Center Rotterdam, Dr Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Jeroen A. A. Demmers
- Proteomics
Center, Erasmus MC, University Medical Center Rotterdam, Dr Molewaterplein
50, 3015 GE Rotterdam, The Netherlands
| | - Arzu Umar
- Department
of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam,
Be401, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
- Postgraduate
School of Molecular Medicine, Erasmus MC, University Medical Center Rotterdam, Dr Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
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17
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Wright EP, Padula MP, Higgins VJ, Aldrich-Wright JR, Coorssen JR. A Systems Biology Approach to Understanding the Mechanisms of Action of an Alternative Anticancer Compound in Comparison to Cisplatin. Proteomes 2014; 2:501-526. [PMID: 28250393 PMCID: PMC5302693 DOI: 10.3390/proteomes2040501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 09/19/2014] [Accepted: 10/29/2014] [Indexed: 01/22/2023] Open
Abstract
Many clinically available anticancer compounds are designed to target DNA. This commonality of action often yields overlapping cellular response mechanisms and can thus detract from drug efficacy. New compounds are required to overcome resistance mechanisms that effectively neutralise compounds like cisplatin and those with similar chemical structures. Studies have shown that 56MESS is a novel compound which, unlike cisplatin, does not covalently bind to DNA, but is more toxic to many cell lines and active against cisplatin-resistant cells. Furthermore, a transcriptional study of 56MESS in yeast has implicated iron and copper metabolism as well as the general yeast stress response following challenge with 56MESS. Beyond this, the cytotoxicity of 56MESS remains largely uncharacterised. Here, yeast was used as a model system to facilitate a systems-level comparison between 56MESS and cisplatin. Preliminary experiments indicated that higher concentrations than seen in similar studies be used. Although a DNA interaction with 56MESS had been theorized, this work indicated that an effect on protein synthesis/ degradation was also implicated in the mechanism(s) of action of this novel anticancer compound. In contrast to cisplatin, the different mechanisms of action that are indicated for 56MESS suggest that this compound could overcome cisplatin resistance either as a stand-alone treatment or a synergistic component of therapeutics.
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Affiliation(s)
- Elise P Wright
- Molecular Physiology Department, and the Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Campbelltown, NSW 2751, Australia.
| | - Matthew P Padula
- Proteomics Core Facility, Faculty of Science, University of Technology, Sydney, NSW 2007, Australia.
| | - Vincent J Higgins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2052, Australia.
| | - Janice R Aldrich-Wright
- Molecular Physiology Department, and the Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Campbelltown, NSW 2751, Australia.
- School of Science and Health, University of Western Sydney, Campbelltown, NSW 2751, Australia.
| | - Jens R Coorssen
- Molecular Physiology Department, and the Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Campbelltown, NSW 2751, Australia.
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18
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Qu Y, Marshall LA, Santiago JG. Simultaneous Purification and Fractionation of Nucleic Acids and Proteins from Complex Samples Using Bidirectional Isotachophoresis. Anal Chem 2014; 86:7264-8. [DOI: 10.1021/ac501299a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yatian Qu
- Department
of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
| | - Lewis A. Marshall
- Department
of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Juan G. Santiago
- Department
of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
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19
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Oliveira BM, Coorssen JR, Martins-de-Souza D. 2DE: the phoenix of proteomics. J Proteomics 2014; 104:140-50. [PMID: 24704856 DOI: 10.1016/j.jprot.2014.03.035] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 03/21/2014] [Accepted: 03/24/2014] [Indexed: 12/22/2022]
Abstract
UNLABELLED Given the rapid developments in mass spectrometry (MS) in terms of sensitivity, mass accuracy, and throughput, some have suggested that two-dimensional gel electrophoresis (2DE) may no longer be a method of choice for proteomic analyses. However, as recognition of issues with these newer shotgun-MS approaches grows, there is a fresh and growing regard for the maturity of 2DE-MS as a genuine top-down analytical approach, particularly as it resolves thousands of intact protein species in a single run, enabling the simultaneous analysis of total protein complement, including isoforms and post-translational modifications. Given the strengths of both, it is most appropriate to view these as complementary or at least parallel approaches: as proteins encompass a myriad of physico-chemical properties, and the real aim is to explore proteomes as deeply as possible, all available resolving strategies must be considered in terms of the complexity encountered. It is time to critically and constructively focus on the optimization and integration of existing techniques rather than simplistically suggesting that one should replace the other. Our intention here is thus to present an overview of protein resolving techniques, focusing on milestones associated with 2DE, including pros, cons, advances and variations, in particular relative to shotgun proteomic approaches. BIOLOGICAL SIGNIFICANCE Proteomic researchers recognize the importance of 2DE in the history of proteomics. But the latest developments in mass spectrometry-based techniques have led some researchers to retire 2DE in their labs. However, we argue here that 2DE-MS is a genuine top-down analytical approach. The significance of this discussion is to make proteomic researchers aware of the importance of this technique in a proteomic pipeline. This article is part of a Special Issue entitled: Environmental and structural proteomics.
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Affiliation(s)
- Bruno M Oliveira
- Catarinense Federal Institute, Videira Campus, Videira, SC, Brazil
| | - Jens R Coorssen
- Dept. of Molecular Physiology, School of Medicine, University of Western Sydney, Australia; UWS Molecular Medicine Research Group, University of Western Sydney, Australia.
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry, Institute of Biology, State University of Campinas (UNICAMP), Campinas, Sao Paulo, Brazil; Laboratory of Neuroscience (LIM-27), Department and Institute of Psychiatry, Faculty of Medicine, University of São Paulo, Brazil; Dept. of Psychiatry and Psychotherapy, Ludwig Maximilians University (LMU), Munich, Germany.
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20
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Wright EP, Partridge MA, Padula MP, Gauci VJ, Malladi CS, Coorssen JR. Top-down proteomics: enhancing 2D gel electrophoresis from tissue processing to high-sensitivity protein detection. Proteomics 2014; 14:872-89. [PMID: 24452924 DOI: 10.1002/pmic.201300424] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 12/01/2013] [Accepted: 12/16/2013] [Indexed: 02/04/2023]
Abstract
The large-scale resolution and detection of proteins from complex native mixtures is fundamental to quantitative proteomic analyses. Comprehensive analyses depend on careful tissue handling and quantitative protein extraction and assessment. To most effectively link these analyses with an understanding of underlying molecular mechanisms, it is critical that all protein types - isoforms, splice variants and those with functionally important PTMs - are quantitatively extracted with high reproducibility. Methodological details concerning protein extraction and resolution using 2DE are discussed with reference to current in-gel protein detection limits. We confirm a significant increase in total protein, and establish that extraction, resolution and detection of phospho- and glycoproteins are improved following automated frozen disruption relative to manual homogenisation. The quality of 2DE protein resolution is established using third-dimension separations and 'deep imaging'; substantially more proteins/protein species than previously realised are actually resolved by 2DE. Thus, the key issue for effective proteome analyses is most likely to be detection, not resolution. Thus, these systematic methodological and technical advances further solidify the role of 2DE in top-down proteomics. By routinely assessing as much proteomic data from a sample as possible, 2DE enables more detailed and critical insights into molecular mechanisms underlying different physiological states.
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Affiliation(s)
- Elise P Wright
- Department of Molecular Physiology, Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Penrith, NSW, Australia
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21
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Wright EP, Prasad KAG, Padula MP, Coorssen JR. Deep imaging: how much of the proteome does current top-down technology already resolve? PLoS One 2014; 9:e86058. [PMID: 24489691 PMCID: PMC3904854 DOI: 10.1371/journal.pone.0086058] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 12/10/2013] [Indexed: 11/21/2022] Open
Abstract
Effective proteome analyses are based on interplay between resolution and detection. It had been claimed that resolution was the main factor limiting the use of two-dimensional gel electrophoresis. Improved protein detection now indicates that this is unlikely to be the case. Using a highly refined protocol, the rat brain proteome was extracted, resolved, and detected. In order to overcome the stain saturation threshold, high abundance protein species were excised from the gel following standard imaging. Gels were then imaged again using longer exposure times, enabling detection of lower abundance, less intensely stained protein species. This resulted in a significant enhancement in the detection of resolved proteins, and a slightly modified digestion protocol enabled effective identification by standard mass spectrometric methods. The data indicate that the resolution required for comprehensive proteome analyses is already available, can assess multiple samples in parallel, and preserve critical information concerning post-translational modifications. Further optimization of staining and detection methods promises additional improvements to this economical, widely accessible and effective top-down approach to proteome analysis.
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Affiliation(s)
- Elise P. Wright
- Molecular Physiology, and the UWS Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Campbelltown, NSW, Australia
| | - Kali A. G. Prasad
- Molecular Physiology, and the UWS Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Campbelltown, NSW, Australia
| | - Matthew P. Padula
- Proteomics Core Facility, Faculty of Science, University of Technology, Sydney, NSW, Australia
| | - Jens R. Coorssen
- Molecular Physiology, and the UWS Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Campbelltown, NSW, Australia
- * E-mail:
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22
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Knigge T, Letendre J, Monsinjon T. Sample preparation for two-dimensional gel electrophoresis: Considering the composition of biological material. Proteomics 2013; 13:3106-2108. [DOI: 10.1002/pmic.201300436] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 10/02/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Thomas Knigge
- Laboratory of Ecotoxicology; Le Havre University; Le Havre France
| | - Julie Letendre
- Laboratory of Ecotoxicology; Le Havre University; Le Havre France
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23
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Butt RH, Coorssen JR. Coomassie blue as a near-infrared fluorescent stain: a systematic comparison with Sypro Ruby for in-gel protein detection. Mol Cell Proteomics 2013; 12:3834-50. [PMID: 24043422 DOI: 10.1074/mcp.m112.021881] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Quantitative proteome analyses suggest that the well-established stain colloidal Coomassie Blue, when used as an infrared dye, may provide sensitive, post-electrophoretic in-gel protein detection that can rival even Sypro Ruby. Considering the central role of two-dimensional gel electrophoresis in top-down proteomic analyses, a more cost effective alternative such as Coomassie Blue could prove an important tool in ongoing refinements of this important analytical technique. To date, no systematic characterization of Coomassie Blue infrared fluorescence detection relative to detection with SR has been reported. Here, seven commercial Coomassie stain reagents and seven stain formulations described in the literature were systematically compared. The selectivity, threshold sensitivity, inter-protein variability, and linear-dynamic range of Coomassie Blue infrared fluorescence detection were assessed in parallel with Sypro Ruby. Notably, several of the Coomassie stain formulations provided infrared fluorescence detection sensitivity to <1 ng of protein in-gel, slightly exceeding the performance of Sypro Ruby. The linear dynamic range of Coomassie Blue infrared fluorescence detection was found to significantly exceed that of Sypro Ruby. However, in two-dimensional gel analyses, because of a blunted fluorescence response, Sypro Ruby was able to detect a few additional protein spots, amounting to 0.6% of the detected proteome. Thus, although both detection methods have their advantages and disadvantages, differences between the two appear to be small. Coomassie Blue infrared fluorescence detection is thus a viable alternative for gel-based proteomics, offering detection comparable to Sypro Ruby, and more reliable quantitative assessments, but at a fraction of the cost.
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24
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Chiu CL, Morgan CT, Lupton SJ, Lind JM. Parent of origin influences the cardiac expression of vascular endothelial growth factor (Vegfa). BMC MEDICAL GENETICS 2013; 14:43. [PMID: 23560444 PMCID: PMC3626619 DOI: 10.1186/1471-2350-14-43] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 03/25/2013] [Indexed: 11/10/2022]
Abstract
Background Vascular endothelial growth factor A (VEGFA) is a major regulator of both physiological and pathological angiogenesis. Associations between polymorphisms in VEGFA and complex disease have been inconsistent. The parent from whom the allele was inherited may account for these inconsistencies. This study examined the parent of origin effect on the expression of murine Vegfa. Methods Two homozygous, inbred mouse strains A/J (AJ) and 129x1/SvJ (129) were crossed to produce reciprocal AJ129 and 129AJ offspring, respectively. RNA was extracted from cardiac tissue of 6 week old male (n = 8) and female (n = 8) parental, and male and female F1 offspring mice (AJ129 n = 8 and 129AJ n = 8). Vegfa and Hif1a expression levels were measured by qPCR and compared between the F1 offspring from the reciprocal crosses. Results We found significant differences in the expression of Vegfa in F1 offspring (AJ129 and 129AJ mice) of the reciprocal crosses between AJ and 129 mice. Offspring of male AJ mice had significantly higher expression of Vegfa than offspring of male 129 mice (p = 0.006). This difference in expression was not the result of preferential allele expression (allelic imbalance). Expression of Hif1a, a transcriptional regulator of Vegfa expression, was also higher in F1 offspring of an AJ father (p = 0.004). Conclusion Differences in Vegfa and Hif1a gene expression are likely the result of an upstream angiogenic regulator gene that is influenced by the parent of origin. These results highlight the importance of including inheritance information, such as parent of origin, when undertaking allelic association studies.
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Affiliation(s)
- Christine L Chiu
- University of Western Sydney, School of Medicine, Penrith, NSW 2751, Locked Bag 1797, Australia.
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25
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Simões AES, Pereira DM, Amaral JD, Nunes AF, Gomes SE, Rodrigues PM, Lo AC, D'Hooge R, Steer CJ, Thibodeau SN, Borralho PM, Rodrigues CMP. Efficient recovery of proteins from multiple source samples after TRIzol(®) or TRIzol(®)LS RNA extraction and long-term storage. BMC Genomics 2013; 14:181. [PMID: 23496794 PMCID: PMC3620933 DOI: 10.1186/1471-2164-14-181] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Accepted: 03/06/2013] [Indexed: 11/10/2022] Open
Abstract
Background Simultaneous isolation of nucleic acids and proteins from a single biological sample facilitates meaningful data interpretation and reduces time, cost and sampling errors. This is particularly relevant for rare human and animal specimens, often scarce, and/or irreplaceable. TRIzol® and TRIzol®LS are suitable for simultaneous isolation of RNA, DNA and proteins from the same biological sample. These reagents are widely used for RNA and/or DNA isolation, while reports on their use for protein extraction are limited, attributable to technical difficulties in protein solubilisation. Results TRIzol®LS was used for RNA isolation from 284 human colon cancer samples, including normal colon mucosa, tubulovillous adenomas, and colon carcinomas with proficient and deficient mismatch repair system. TRIzol® was used for RNA isolation from human colon cancer cells, from brains of transgenic Alzheimer’s disease mice model, and from cultured mouse cortical neurons. Following RNA extraction, the TRIzol®-chloroform fractions from human colon cancer samples and from mouse hippocampus and frontal cortex were stored for 2 years and 3 months, respectively, at −80°C until used for protein isolation. Simple modifications to the TRIzol® manufacturer’s protocol, including Urea:SDS solubilization and sonication, allowed improved protein recovery yield compared to the TRIzol® manufacturer’s protocol. Following SDS-PAGE and Ponceau and Coomassie staining, recovered proteins displayed wide molecular weight range and staining pattern comparable to those obtainable with commonly used protein extraction protocols. We also show that nuclear and cytosolic proteins can be easily extracted and detected by immunoblotting, and that posttranslational modifications, such as protein phosphorylation, are detectable in proteins recovered from TRIzol®-chloroform fractions stored for up to 2 years at −80°C. Conclusions We provide a novel approach to improve protein recovery from samples processed for nucleic acid extraction with TRIzol® and TRIzol®LS compared to the manufacturer`s protocol, allowing downstream immunoblotting and evaluation of steady-state relative protein expression levels. The method was validated in large sets of samples from multiple sources, including human colon cancer and brains of transgenic Alzheimer’s disease mice model, stored in TRIzol®-chloroform for up to two years. Collectively, we provide a faster and cheaper alternative to the TRIzol® manufacturer`s protein extraction protocol, illustrating the high relevance, and wide applicability, of the present protein isolation method for the immunoblot evaluation of steady-state relative protein expression levels in samples from multiple sources, and following prolonged storage.
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Affiliation(s)
- André E S Simões
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
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Gauci VJ, Padula MP, Coorssen JR. Coomassie blue staining for high sensitivity gel-based proteomics. J Proteomics 2013; 90:96-106. [PMID: 23428344 DOI: 10.1016/j.jprot.2013.01.027] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 01/27/2013] [Indexed: 11/26/2022]
Abstract
Gel electrophoresis, particularly one- (1DE) and two-dimensional electrophoresis (2DE), remain among the most widely used top-down methods for resolving and analysing proteomes. Detection of the resulting protein maps relies on staining (i.e. colloidal coomassie blue (CCB) or SYPRO Ruby (SR), in addition to many others). Fluorescent in-gel protein stains are generally preferred for higher sensitivity, reduced background, and wider dynamic range. Although traditionally used for densitometry, CBB has fluorescent properties. Indeed, infrared detection of CCB stained protein was comparable to SR, with BioSafe (Bio-Rad) and the Neuhoff formulation (NCCB) identified as potentially superior to SR; a minor sensitivity issue encountered in gel-resolved proteomes; might have been due to the unified staining protocol used. Here the staining protocol for both CCB formulations was optimised, yielding improved selectivity without affecting sensitivity; the resulting linear dynamic range was similar for BioSafe and NCCB and somewhat better than SR. 2D gel-based analyses of mouse brain and Arabidopsis thaliana (leaf) proteomes indicated markedly superior spot detection using the NCCB formulation. Thus more sensitive, quantitative in-gel protein analyses can be achieved using NCCB, at a fraction of the cost.
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Affiliation(s)
- Victoria J Gauci
- Molecular Physiology, and the Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Sydney, Australia
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27
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Young C, Truman P. Proteins isolated with TRIzol are compatible with two-dimensional electrophoresis and mass spectrometry analyses. Anal Biochem 2012; 421:330-2. [DOI: 10.1016/j.ab.2011.10.045] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 10/16/2011] [Accepted: 10/27/2011] [Indexed: 12/01/2022]
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28
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Nakashima AS, Hussain Butt R, Dyck RH. Alterations in protein and gene expression within the barrel cortices of ZnT3 knockout mice: Experience-independent and dependent changes. Neurochem Int 2011; 59:860-70. [DOI: 10.1016/j.neuint.2011.08.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 07/27/2011] [Accepted: 08/08/2011] [Indexed: 12/12/2022]
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29
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Gauci VJ, Wright EP, Coorssen JR. Quantitative proteomics: assessing the spectrum of in-gel protein detection methods. J Chem Biol 2011; 4:3-29. [PMID: 21686332 PMCID: PMC3022124 DOI: 10.1007/s12154-010-0043-5] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Accepted: 06/02/2010] [Indexed: 11/28/2022] Open
Abstract
Proteomics research relies heavily on visualization methods for detection of proteins separated by polyacrylamide gel electrophoresis. Commonly used staining approaches involve colorimetric dyes such as Coomassie Brilliant Blue, fluorescent dyes including Sypro Ruby, newly developed reactive fluorophores, as well as a plethora of others. The most desired characteristic in selecting one stain over another is sensitivity, but this is far from the only important parameter. This review evaluates protein detection methods in terms of their quantitative attributes, including limit of detection (i.e., sensitivity), linear dynamic range, inter-protein variability, capacity for spot detection after 2D gel electrophoresis, and compatibility with subsequent mass spectrometric analyses. Unfortunately, many of these quantitative criteria are not routinely or consistently addressed by most of the studies published to date. We would urge more rigorous routine characterization of stains and detection methodologies as a critical approach to systematically improving these critically important tools for quantitative proteomics. In addition, substantial improvements in detection technology, particularly over the last decade or so, emphasize the need to consider renewed characterization of existing stains; the quantitative stains we need, or at least the chemistries required for their future development, may well already exist.
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Affiliation(s)
- Victoria J. Gauci
- Molecular Physiology, School of Medicine, and Molecular Medicine Research Group, University of Western Sydney, Campbelltown, NSW 1797 Australia
| | - Elise P. Wright
- Molecular Physiology, School of Medicine, and Molecular Medicine Research Group, University of Western Sydney, Campbelltown, NSW 1797 Australia
| | - Jens R. Coorssen
- Molecular Physiology, School of Medicine, and Molecular Medicine Research Group, University of Western Sydney, Campbelltown, NSW 1797 Australia
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OKAMOTO H, UMEDA S, NOZAWA T, SUZUKI MT, YOSHIKAWA Y, MATSUURA ET, IWATA T. Comparative Proteomic Analyses of Macular and Peripheral Retina of Cynomolgus Monkeys (Macaca fascicularis). Exp Anim 2010; 59:171-82. [DOI: 10.1538/expanim.59.171] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Affiliation(s)
- Haru OKAMOTO
- Division of Molecular & Cellular Biology, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center
- Department of Advanced Biosciences, Ochanomizu University
| | - Shinsuke UMEDA
- Division of Molecular & Cellular Biology, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center
| | | | | | - Yasuhiro YOSHIKAWA
- Department of Biomedical Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | | | - Takeshi IWATA
- Division of Molecular & Cellular Biology, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center
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Lu A, Wiśniewski JR, Mann M. Comparative proteomic profiling of membrane proteins in rat cerebellum, spinal cord, and sciatic nerve. J Proteome Res 2009; 8:2418-25. [PMID: 19290618 DOI: 10.1021/pr8010364] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Proteomics is an increasingly powerful technology that can provide in-depth insights into entire proteomes and their variation upon disease. Large-scale proteomics today enables identification and measurement of changes of thousands of proteins from minute amount of tissues. Here, we provide a proteomic profile of three distinct parts of the murine nerve system: cerebellum, spinal cord, and sciatic nerve. We focus on membrane proteins as the key regulators of neural transmission and memory. Rat tissues were homogenized and extracted to remove nonmembrane proteins and the resulting membranes were solubilized with detergents. Proteins were fractionated by size exclusion chromatography, depleted for detergents, digested and analyzed by LC-MS/MS using the LTQ-Orbitrap instrument. With the application of stringent identification criteria, in total, 4124 proteins were identified. Of these proteins, 3528, 3290, and 1649 were mapped to cerebellum, spinal cord, and sciatic nerve, respectively, allowing in-depth mapping of neurotransmitter receptors, ion channels, and transporter proteins. This work is the most in-depth proteomic analysis of nerve tissues to date and provides the first unbiased insights into the proteomes of anatomically and functionally distinct parts of the membrane proteome of the central and peripheral nerve systems. The methods applied here can be directly applied to studying nerve systems and their disorders.
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Affiliation(s)
- Aiping Lu
- Department of Proteomics and Signal Transduction, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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Rader JS, Malone JP, Gross J, Gilmore P, Brooks RA, Nguyen L, Crimmins DL, Feng S, Wright JD, Taylor N, Zighelboim I, Funk MC, Huettner PC, Ladenson JH, Gius D, Townsend RR. A unified sample preparation protocol for proteomic and genomic profiling of cervical swabs to identify biomarkers for cervical cancer screening. Proteomics Clin Appl 2008; 2:1658-69. [PMID: 21136816 DOI: 10.1002/prca.200780146] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2007] [Indexed: 01/04/2023]
Abstract
Cervical cancer screening is ideally suited for the development of biomarkers due to the ease of tissue acquisition and the well-established histological transitions. Furthermore, cell and biologic fluid obtained from cervix samples undergo specific molecular changes that can be profiled. However, the ideal manner and techniques for preparing cervical samples remains to be determined. To address this critical issue a patient screening protein and nucleic acid collection protocol was established. RNAlater was used to collect the samples followed by proteomic methods to identify proteins that were differentially expressed in normal cervical epithelial versus cervical cancer cells. Three hundred ninety spots were identified via 2-D DIGE that were expressed at either higher or lower levels (>three-fold) in cervical cancer samples. These proteomic results were compared to genes in a cDNA microarray analysis of microdissected neoplastic cervical specimens to identify overlapping patterns of expression. The most frequent pathways represented by the combined dataset were: cell cycle: G2/M DNA damage checkpoint regulation; aryl hydrocarbon receptor signaling; p53 signaling; cell cycle: G1/S checkpoint regulation; and the ER stress pathway. HNRPA2B1 was identified as a biomarker candidate with increased expression in cancer compared to normal cervix and validated by Western blot.
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Affiliation(s)
- Janet S Rader
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Washington University School of Medicine and Alvin J. Siteman Cancer Center, St. Louis, MO, USA; Department of Genetics, Washington University School of Medicine and Alvin J. Siteman Cancer Center, St. Louis, MO, USA.
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