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Lin Y, Cheng Q, Wei T. Surface engineering of lipid nanoparticles: targeted nucleic acid delivery and beyond. BIOPHYSICS REPORTS 2023; 9:255-278. [PMID: 38516300 PMCID: PMC10951480 DOI: 10.52601/bpr.2023.230022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 11/28/2023] [Indexed: 03/23/2024] Open
Abstract
Harnessing surface engineering strategies to functionalize nucleic acid-lipid nanoparticles (LNPs) for improved performance has been a hot research topic since the approval of the first siRNA drug, patisiran, and two mRNA-based COVID-19 vaccines, BNT162b2 and mRNA-1273. Currently, efforts have been mainly made to construct targeted LNPs for organ- or cell-type-specific delivery of nucleic acid drugs by conjugation with various types of ligands. In this review, we describe the surface engineering strategies for nucleic acid-LNPs, considering ligand types, conjugation chemistries, and incorporation methods. We then outline the general purification and characterization techniques that are frequently used following the engineering step and emphasize the specific techniques for certain types of ligands. Next, we comprehensively summarize the currently accessible organs and cell types, as well as the other applications of the engineered LNPs. Finally, we provide considerations for formulating targeted LNPs and discuss the challenges of successfully translating the "proof of concept" from the laboratory into the clinic. We believe that addressing these challenges could accelerate the development of surface-engineered LNPs for targeted nucleic acid delivery and beyond.
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Affiliation(s)
- Yi Lin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China
| | - Qiang Cheng
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China
| | - Tuo Wei
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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2
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Singh VK, Srivastava M, Seed TM. Protein biomarkers for radiation injury and testing of medical countermeasure efficacy: promises, pitfalls, and future directions. Expert Rev Proteomics 2023; 20:221-246. [PMID: 37752078 DOI: 10.1080/14789450.2023.2263652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/11/2023] [Indexed: 09/28/2023]
Abstract
INTRODUCTION Radiological/nuclear accidents, hostile military activity, or terrorist strikes have the potential to expose a large number of civilians and military personnel to high doses of radiation resulting in the development of acute radiation syndrome and delayed effects of exposure. Thus, there is an urgent need for sensitive and specific assays to assess the levels of radiation exposure to individuals. Such radiation exposures are expected to alter primary cellular proteomic processes, resulting in multifaceted biological responses. AREAS COVERED This article covers the application of proteomics, a promising and fast developing technology based on quantitative and qualitative measurements of protein molecules for possible rapid measurement of radiation exposure levels. Recent advancements in high-resolution chromatography, mass spectrometry, high-throughput, and bioinformatics have resulted in comprehensive (relative quantitation) and precise (absolute quantitation) approaches for the discovery and accuracy of key protein biomarkers of radiation exposure. Such proteome biomarkers might prove useful for assessing radiation exposure levels as well as for extrapolating the pharmaceutical dose of countermeasures for humans based on efficacy data generated using animal models. EXPERT OPINION The field of proteomics promises to be a valuable asset in evaluating levels of radiation exposure and characterizing radiation injury biomarkers.
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Affiliation(s)
- Vijay K Singh
- Division of Radioprotectants, Department of Pharmacology and Molecular Therapeutics, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Meera Srivastava
- Department of Anatomy, Physiology and Genetics, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
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Dowling P, Gargan S, Swandulla D, Ohlendieck K. Fiber-Type Shifting in Sarcopenia of Old Age: Proteomic Profiling of the Contractile Apparatus of Skeletal Muscles. Int J Mol Sci 2023; 24:ijms24032415. [PMID: 36768735 PMCID: PMC9916839 DOI: 10.3390/ijms24032415] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
The progressive loss of skeletal muscle mass and concomitant reduction in contractile strength plays a central role in frailty syndrome. Age-related neuronal impairments are closely associated with sarcopenia in the elderly, which is characterized by severe muscular atrophy that can considerably lessen the overall quality of life at old age. Mass-spectrometry-based proteomic surveys of senescent human skeletal muscles, as well as animal models of sarcopenia, have decisively improved our understanding of the molecular and cellular consequences of muscular atrophy and associated fiber-type shifting during aging. This review outlines the mass spectrometric identification of proteome-wide changes in atrophying skeletal muscles, with a focus on contractile proteins as potential markers of changes in fiber-type distribution patterns. The observed trend of fast-to-slow transitions in individual human skeletal muscles during the aging process is most likely linked to a preferential susceptibility of fast-twitching muscle fibers to muscular atrophy. Studies with senescent animal models, including mostly aged rodent skeletal muscles, have confirmed fiber-type shifting. The proteomic analysis of fast versus slow isoforms of key contractile proteins, such as myosin heavy chains, myosin light chains, actins, troponins and tropomyosins, suggests them as suitable bioanalytical tools of fiber-type transitions during aging.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Stephen Gargan
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Dieter Swandulla
- Institute of Physiology, University of Bonn, D53115 Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Correspondence: ; Tel.: +353-1-7083842
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Mosavi Z, Bashi Zadeh Fakhar H, Rezaei-Tavirani M, Akbari ME, Rostami F. Proteome profiling of ductal carcinoma in situ. Breast Dis 2023; 41:513-520. [PMID: 36641653 DOI: 10.3233/bd-220017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
BACKGROUND AND AIM DCIS is the most common type of non-invasive breast cancer, accounting for about 15 to 30%. Proteome profile is used to detect biomarkers in the tissues of breast cancer patients by mass spectrometry. This study aimed to obtain the expression profile of DCIS proteome, and the expression profile of invasive biomarkers, and finally to introduce a dedicated biomarker panel to facilitate the prognosis and early detection for in situ breast cancer patients. METHODS AND MATERIALS In this study, 10 patients with breast cancer (DCIS) were studied. Benign (marginal) and cancerous tissue samples were obtained from patients for proteomics experiments. Initially, all tissue proteins were extracted using standard methods, and the proteins were separated using two-dimensional electrophoresis. Then, the expression amount of the extracted proteins was determined by ITRAQ. The data were analysed by R software, and gene ontology was utilised for describing the protein in detail. RESULTS 30 spots on gel electrophoresis were found in the tumor tissue group (sample), and 15 spots in the margin group (control) with P < 0.05. Healthy and cancerous tissue gels showed that 5 spots had different expression. VWF, MMP9, ITGAM, MPO and PLG protein spots were identified using the site www.ebi.ac.uk/IPI. Finally, protein biomarkers for breast tumor tissue with margin were introduced with the names of P04406, P49915, P05323, P06733, and P02768. DISCUSSION There are 5 critical proteins in inducing cancer pathways especially complement and coagulation cascades. The hall markers of a healthy cell to be cancerous are proliferation, invasion, angiogenesis, and changes in the immune system. Hence, regulation of protein plays a key role in developing recurrence to breast cancer in margins.
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Affiliation(s)
- Zeinb Mosavi
- Department of Medical Science, Islamic Azad University, Chalus Branch, Chalous, Iran
| | - Haniyeh Bashi Zadeh Fakhar
- Cancer Research Centre (CRC), Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Laboratory Science, Islamic Azad University, Chalous Branch, Chalous, Iran
| | | | - Mohamd Esmaeel Akbari
- Cancer Research Centre (CRC), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Forouzan Rostami
- Department of Nursing, Faculty of Nursing and Midwifery, Islamic Azad University, Chalous, Iran
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Abstract
The gradual loss of skeletal muscle mass during aging and associated decline in contractile strength can result in reduced fitness, frailty, and loss of independence. In order to better understand the molecular and cellular mechanisms that underlie sarcopenia of old age and the frailty syndrome, as well as identify novel therapeutic targets to treat age-related fiber wasting, it is crucial to develop a comprehensive biomarker signature of muscle aging. Fluorescence two-dimensional gel electrophoresis (2D-DIGE) in combination with sensitive mass spectrometry presents an ideal bioanalytical tool for biomarker discovery in biogerontology. This chapter outlines the application of the 2D-DIGE method for the comparative analysis of human biopsy specimens from middle-aged versus senescent individuals using a two-CyDye-based method.
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Affiliation(s)
- Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
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Barreiro C, Ibáñez AM. Bidimensional Analyses of the Intra- and Extracellular Proteomes of Steroid Producer Mycobacteria. Methods Mol Biol 2023; 2704:115-141. [PMID: 37642841 DOI: 10.1007/978-1-0716-3385-4_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The importance of the pathogenic mycobacteria has mainly focused the omic analyses on different aspects of their clinical significance. However, those industrially relevant mycobacteria have received less attention, even though the steroid market sales in 2021 were estimated in $56.45 billion.The extracellular proteome, due to its relevance in the sterol processing and uptake, and the intracellular proteome, because of its role in steroids bioconversion, are the core of the present chapter. Both, monodimensional gels, as preparatory analysis, and bidimensional gels as proteome analysis are described. As a proof of concept, the protein extraction methods for both sub-proteomes of Mycobacterium are described. Thus, procedures and relevant key points of these proteome analyses are fully detailed.
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Affiliation(s)
- Carlos Barreiro
- Área de Bioquímica y Biología Molecular, Departamento de Biología Molecular, Facultad de Veterinaria, Universidad de León, León, Spain.
| | - Ana M Ibáñez
- Instituto de Investigación de la Viña y el Vino, Escuela de Ingeniería Agraria, Universidad de León, León, Spain
- Instituto Tecnológico Agrario de Castilla y León (ITACyL), Área de Investigación Agrícola, Valladolid, Spain
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Abstract
The combination of large-scale protein separation techniques, sophisticated mass spectrometry, and systems bioinformatics has led to the establishment of proteomics as a distinct discipline within the wider field of protein biochemistry. Both discovery proteomics and targeted proteomics are widely used in biological and biomedical research, whereby the analytical approaches can be broadly divided into proteoform-centric top-down proteomics versus peptide-centric bottom-up proteomics. This chapter outlines the scientific value of top-down proteomics and describes how fluorescence two-dimensional difference gel electrophoresis can be combined with the systematic analysis of crucial post-translational modifications. The concept of on-membrane digestion following the electrophoretic transfer of proteins and the usefulness of comparative two-dimensional immunoblotting are discussed.
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Affiliation(s)
- Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
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Abstract
The skeletal muscle proteome consists of a large number of diverse protein species with a broad and dynamic concentration range. Since mature skeletal muscles are characterized by a distinctive combination of contractile cells with differing physiological and biochemical properties, it is essential to determine specific differences in the protein composition of fast, slow, and hybrid fibers. Fluorescence two-dimensional difference gel electrophoresis (2D-DIGE) is a powerful comparative tool to analyze fiber type-specific differences between predominantly fast contracting versus slower twitching muscles. In this chapter, the application of the 2D-DIGE method for the comparative analysis of different subtypes of skeletal muscles is outlined in detail. A standardized proteomic workflow is described, involving sample preparation, protein extraction, differential fluorescence labeling using a 3-CyDye system, first-dimension isoelectric focusing, second-dimension slab gel electrophoresis, 2D-DIGE image analysis, protein digestion, and mass spectrometry.
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Affiliation(s)
- Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
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Abstract
Fluorescence two-dimensional difference gel electrophoresis (2D-DIGE) is a widely employed method for efficient protein separation and the determination of abundance changes in distinct proteoforms. This makes this gel-based method a key technique of comparative approaches in top-down proteomics. For the appropriate screening of proteome-wide alterations, initial preparative steps involve sample handling, homogenization, subcellular fractionation, and the determination of protein concentration, which makes the optimal application of these techniques a crucial part of a successful initiation of a new 2D-DIGE-based analysis. This chapter describes sample homogenization and a standardized protein assay for the preparation of homogenates with a known protein concentration for subsequent differential fluorescent tagging and two-dimensional gel electrophoretic separation.
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Affiliation(s)
- Stephen Gargan
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
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Tsai YT, Ruan JW, Chang CS, Ko ML, Chou HC, Lin CC, Lin CM, Huang CT, Wei YS, Liao EC, Chen HY, Lin LH, Lin MW, Kao CY, Chan HL. Proteomic and microbial assessments on the effect of Antrodia cinnamomea in C57BL/6 mice. Arch Biochem Biophys 2021; 713:109058. [PMID: 34627749 DOI: 10.1016/j.abb.2021.109058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 10/03/2021] [Accepted: 10/05/2021] [Indexed: 01/01/2023]
Abstract
Antrodia cinnamomea (AC) is a nutraceutical fungus and studies have suggested that AC has the potential to prevent or alleviate diseases. However, little is known about the AC-induced phenotypes on the intestine-liver axis and gut microbial alterations. Here, we performed two-dimensional difference gel electrophoresis (2D-DIGE) and MALDI-Biotyper to elaborate the AC-induced phenotypes on the intestine-liver axis and gut microbial distribution of C57BL/6 mice. The experimental outcomes showed that the hepatic density may increase by elevating hepatic redox regulation, lipid degradation and glycolysis-related proteins and alleviating cholesterol biosynthesis and transport-related proteins in C57BL/6 mice with AC treatment. Moreover, AC facilitates intestinal glycolysis, TCA cycle, redox and cytoskeleton regulation-related proteins, but also reduces intestinal vesicle transport-related proteins in C57BL/6 mice. However, the body weight, GTT, daily food/water intake, and fecal/urine weight were unaffected by AC supplementation in C57BL/6 mice. Notably, the C57BL/6-AC mice had a higher gut microbial abundance of Alistipes shahii (AS) than C57BL/6-Ctrl mice. In summary, the AC treatment affects intestinal permeability by regulating redox and cytoskeleton-related proteins and elevates the gut microbial abundance of AS in C57BL/6 mice that might be associated with increasing hepatic density and metabolism-related proteins of the liver in C57BL/6 mice. Our study provides an insight into the mechanisms of AC-induced phenotypes and a comprehensive assessment of AC's nutraceutical effect in C57BL/6 mice.
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Affiliation(s)
- Yi-Ting Tsai
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan.
| | - Jhen-Wei Ruan
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan, 70101, Taiwan.
| | - Cherng-Shyang Chang
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan.
| | - Mei-Lan Ko
- Department of Ophthalmology, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, 30059, Taiwan.
| | - Hsiu-Chuan Chou
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu, 30013, Taiwan.
| | - Chi-Chien Lin
- Department of Life Sciences, Institute of Biomedical Science, National Chung Hsing University, Taichung, 402, Taiwan.
| | - Chiao-Mei Lin
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan.
| | - Chih-Ting Huang
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan.
| | - Yu-Shan Wei
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan.
| | - En-Chi Liao
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan.
| | - Hsin-Yi Chen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan.
| | - Li-Hsun Lin
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan.
| | - Meng-Wei Lin
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan.
| | - Cheng-Yuan Kao
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan.
| | - Hong-Lin Chan
- Institute of Bioinformatics and Structural Biology and Department of Medical Sciences, National Tsing Hua University, Hsinchu, 30013, Taiwan.
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Proteomic Research on the Antitumor Properties of Medicinal Mushrooms. Molecules 2021; 26:molecules26216708. [PMID: 34771120 PMCID: PMC8588050 DOI: 10.3390/molecules26216708] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/27/2021] [Accepted: 11/02/2021] [Indexed: 12/22/2022] Open
Abstract
Medicinal mushrooms are increasingly being recognized as an important therapeutic modality in complementary oncology. Until now, more than 800 mushroom species have been known to possess significant pharmacological properties, of which antitumor and immunomodulatory properties have been the most researched. Besides a number of medicinal mushroom preparations being used as dietary supplements and nutraceuticals, several isolates from mushrooms have been used as official antitumor drugs in clinical settings for several decades. Various proteomic approaches allow for the identification of a large number of differentially regulated proteins serendipitously, thereby providing an important platform for a discovery of new potential therapeutic targets and approaches as well as biomarkers of malignant disease. This review is focused on the current state of proteomic research into antitumor mechanisms of some of the most researched medicinal mushroom species, including Phellinus linteus, Ganoderma lucidum, Auricularia auricula, Agrocybe aegerita, Grifola frondosa, and Lentinus edodes, as whole body extracts or various isolates, as well as of complex extract mixtures.
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Carbonara K, Andonovski M, Coorssen JR. Proteomes Are of Proteoforms: Embracing the Complexity. Proteomes 2021; 9:38. [PMID: 34564541 PMCID: PMC8482110 DOI: 10.3390/proteomes9030038] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/24/2021] [Accepted: 08/29/2021] [Indexed: 12/17/2022] Open
Abstract
Proteomes are complex-much more so than genomes or transcriptomes. Thus, simplifying their analysis does not simplify the issue. Proteomes are of proteoforms, not canonical proteins. While having a catalogue of amino acid sequences provides invaluable information, this is the Proteome-lite. To dissect biological mechanisms and identify critical biomarkers/drug targets, we must assess the myriad of proteoforms that arise at any point before, after, and between translation and transcription (e.g., isoforms, splice variants, and post-translational modifications [PTM]), as well as newly defined species. There are numerous analytical methods currently used to address proteome depth and here we critically evaluate these in terms of the current 'state-of-the-field'. We thus discuss both pros and cons of available approaches and where improvements or refinements are needed to quantitatively characterize proteomes. To enable a next-generation approach, we suggest that advances lie in transdisciplinarity via integration of current proteomic methods to yield a unified discipline that capitalizes on the strongest qualities of each. Such a necessary (if not revolutionary) shift cannot be accomplished by a continued primary focus on proteo-genomics/-transcriptomics. We must embrace the complexity. Yes, these are the hard questions, and this will not be easy…but where is the fun in easy?
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Affiliation(s)
| | | | - Jens R. Coorssen
- Faculties of Applied Health Sciences and Mathematics & Science, Departments of Health Sciences and Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada; (K.C.); (M.A.)
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Rossi F, L'Imperio V, Marti HP, Svarstad E, Smith A, Bolognesi MM, Magni F, Pagni F, Pieruzzi F. Proteomics for the study of new biomarkers in Fabry disease: State of the art. Mol Genet Metab 2021; 132:86-93. [PMID: 33077353 DOI: 10.1016/j.ymgme.2020.10.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/08/2020] [Accepted: 10/11/2020] [Indexed: 12/25/2022]
Abstract
Nephropathy represents a major complication of Fabry Disease and its accurate characterization is of paramount importance in predicting the disease progression and assessing the therapeutic responses. The diagnostic process still relies on performing renal biopsy, nevertheless many efforts have been made to discover early reliable biomarkers allowing us to avoid invasive procedures. In this field, proteomics offers a sensitive and fast method leading to an accurate detection of specific pathological proteins and the discovery of diagnostic and prognostic biomarkers that reflect disease progression and facilitate the evaluation of therapeutic responses. Here, we report a review of selected literature focusing on the investigation of several proteomic techniques highlighting their advantages, limitations and future perspectives in their application in the routine study of Fabry Nephropathy.
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Affiliation(s)
- Federica Rossi
- Department of Medicine and Surgery, University of Milano-Bicocca, Nephrology and Dialysis Unit, San Gerardo Hospital, Via G.B. Pergolesi 33, Monza, Italy.
| | - Vincenzo L'Imperio
- Department of Medicine and Surgery, University of Milano-Bicocca, Pathology, San Gerardo Hospital, Via G.B. Pergolesi 33, Monza, Italy.
| | - Hans-Peter Marti
- Department of Medicine, Haukeland University Hospital, Jonas Lies Vei 65, Bergen, Norway; Department of Clinical Medicine, University of Bergen, Jonas Lies Vei 87, Bergen, Norway
| | - Einar Svarstad
- Department of Clinical Medicine, University of Bergen, Jonas Lies Vei 87, Bergen, Norway
| | - Andrew Smith
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano-Bicocca, Via Raoul Follereau 3, Vedano al Lambro, Italy
| | - Maddalena Maria Bolognesi
- Department of Medicine and Surgery, University of Milano-Bicocca, Pathology, San Gerardo Hospital, Via G.B. Pergolesi 33, Monza, Italy
| | - Fulvio Magni
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano-Bicocca, Via Raoul Follereau 3, Vedano al Lambro, Italy
| | - Fabio Pagni
- Department of Medicine and Surgery, University of Milano-Bicocca, Pathology, San Gerardo Hospital, Via G.B. Pergolesi 33, Monza, Italy
| | - Federico Pieruzzi
- Department of Medicine and Surgery, University of Milano-Bicocca, Nephrology and Dialysis Unit, San Gerardo Hospital, Via G.B. Pergolesi 33, Monza, Italy
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14
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Marsilio S, Dröes FC, Dangott L, Chow B, Hill S, Ackermann M, Estep JS, Lidbury JA, Suchodolski JS, Steiner JM. Characterization of the intestinal mucosal proteome in cats with inflammatory bowel disease and alimentary small cell lymphoma. J Vet Intern Med 2021; 35:179-189. [PMID: 33471936 PMCID: PMC7848303 DOI: 10.1111/jvim.16003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 11/27/2020] [Accepted: 12/03/2020] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Current tests for diagnosis and differentiation of lymphoplasmacytic enteritis (LPE) and small cell lymphoma (SCL) in cats are expensive, invasive, and lack specificity. The identification of less invasive, more reliable biomarkers would facilitate diagnosis. OBJECTIVES To characterize the mucosal proteome in endoscopically obtained, small intestinal tissue biopsy specimens. We hypothesized that differentially expressed proteins could be identified and serve as biomarker candidates for the differentiation of LPE and SCL in cats. ANIMALS Six healthy control cats, 6 cats with LPE, and 8 cats with SCL. METHODS The mucosal proteome was analyzed using 2-dimensional fluorescence difference gel electrophoresis (2D DIGE) and nanoflow liquid chromatography tandem mass spectrometry. For 5 proteins, results were verified by Western blot analysis. RESULTS A total of 2349 spots were identified, of which 9 were differentially expressed with a ≥2-fold change between healthy cats and cats with LPE and SCL (.01 < P < .001). Eight of these 9 spots were also differentially expressed between cats with LPE and cats with SCL (P .001 < P < .04). However, Western blot analysis for malate dehydrogenase-1, malate dehydrogenase-2, apolipoprotein, annexin IV, and annexin V did not confirm significant differential protein expression for any of the 5 proteins assessed. CONCLUSIONS AND CLINICAL IMPORTANCE Two-D DIGE did not identify potential biomarker candidates in the intestinal mucosa of cats with LPE and SCL. Future studies should focus on different techniques to identify biomarker candidates for cats with chronic enteropathies (CE).
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Affiliation(s)
- Sina Marsilio
- Department of Medicine and EpidemiologySchool of Veterinary Medicine, University of CaliforniaDavisCAUSA
- Gastrointestinal Laboratory, Department of Small Animal Clinical SciencesTexas A&M College of Veterinary Medicine & Biomedical Sciences, Texas A&M UniversityCollege StationTexasUSA
| | - Floris C. Dröes
- Gastrointestinal Laboratory, Department of Small Animal Clinical SciencesTexas A&M College of Veterinary Medicine & Biomedical Sciences, Texas A&M UniversityCollege StationTexasUSA
| | - Lawrence Dangott
- Protein Chemistry Laboratory, Department of Biochemistry & BiophysicsTexas A&M UniversityCollege StationTexasUSA
| | - Betty Chow
- Veterinary Specialty HospitalSan DiegoCaliforniaUSA
- VCA Animal Specialty & Emergency CenterLos AngelesCaliforniaUSA
| | - Steve Hill
- Veterinary Specialty HospitalSan DiegoCaliforniaUSA
- Flagstaff Veterinary Internal Medicine ConsultingFlagstaffArizonaUSA
| | - Mark Ackermann
- Oregon Veterinary Diagnostic LaboratoryCarlson College of Veterinary Medicine, Oregon State UniversityCorvallisOregonUSA
| | | | - Jonathan A. Lidbury
- Gastrointestinal Laboratory, Department of Small Animal Clinical SciencesTexas A&M College of Veterinary Medicine & Biomedical Sciences, Texas A&M UniversityCollege StationTexasUSA
| | - Jan S. Suchodolski
- Gastrointestinal Laboratory, Department of Small Animal Clinical SciencesTexas A&M College of Veterinary Medicine & Biomedical Sciences, Texas A&M UniversityCollege StationTexasUSA
| | - Jörg M. Steiner
- Gastrointestinal Laboratory, Department of Small Animal Clinical SciencesTexas A&M College of Veterinary Medicine & Biomedical Sciences, Texas A&M UniversityCollege StationTexasUSA
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15
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Bonar E, Chlebicka K, Dubin G, Wladyka B. Application of Two-Dimensional Difference Gel Electrophoresis in Identification of Factors Responsible for Virulence of Staphylococcus aureus. Methods Mol Biol 2020; 2069:139-154. [PMID: 31523772 DOI: 10.1007/978-1-4939-9849-4_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Staphylococcus aureus is a dangerous opportunistic pathogen of humans and animals. Highly virulent and multi-antibiotic-resistant strains are of particular concern due to high invasiveness and limited array of useful treatment options. Proteomics allows identification and investigation of staphylococcal virulence factors to better understand and treat the related disease. Two-dimensional difference gel electrophoresis (2D DIGE) is a powerful method for identification of differences in staphylococcal proteomes, both intracellular and secretory. Not only the presence of particular proteins and their quantities may be determined, but also each modification changing the molecular mass and/or isoelectric point of a protein is trackable. Especially, 2D DIGE allows for detection of posttranslational modifications, including processing and degradation by proteases. For differential analysis, protein samples are labeled with spectrally distinguishable fluorescent dyes, mixed and separated according to their isoelectric point (first dimension), and then electrophoresed in the presence of sodium dodecyl sulfate according to their molecular mass (second dimension). Exceptional resolution of 2D DIGE allows to obtain focused and sharp protein spots, and identify a large number of differentiating proteins. Here we provide protocols for TRI Reagent-based preparation of high-quality samples for 2D DIGE, sample separation, and ways of handling differentiating protein spots which lead to samples ready for protein identification using MS.
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Affiliation(s)
- Emilia Bonar
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Kinga Chlebicka
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Benedykt Wladyka
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
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Rehiman SH, Lim SM, Lim FT, Chin AV, Tan MP, Kamaruzzaman SB, Ramasamy K, Abdul Majeed AB. Fibrinogen isoforms as potential blood-based biomarkers of Alzheimer's disease using a proteomics approach. Int J Neurosci 2020; 132:1014-1025. [PMID: 33280461 DOI: 10.1080/00207454.2020.1860038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Objective: Alzheimer's disease (AD), the commonest form of dementia which is characterized by progressive decline in cognitive function, can only be definitively diagnosed after death. Although biomarkers may aid diagnosis, currently available AD biomarkers, which are predominantly based on cerebrospinal fluid and neuroimaging facilities, are either invasive or costly. Blood-based biomarkers for AD diagnosis are highly sought after due to its practicality at the clinic. This study was undertaken to determine the differential protein expression in plasma amongst Malaysian AD, mild cognitive impairment (MCI) and non-AD individuals. Methods: A proteomic approach which utilized two-dimensional differential in gel electrophoresis (2 D DIGE) was performed for blood samples from 15 AD, 14 MCI and 15 non-AD individuals. Results: Mass spectrometry (MS)-based protein identification via MALDI ToF/ToF showed that fibrinogen-β-chain (spot 64) and fibrinogen-γ-chain (spot 91) with differential expression ratio >1.5 were significantly upregulated (p < 0.05) in AD patients when compared to non-AD individuals. Further data analysis using Pearson correlation found that the upregulated fibrinogen-γ-chain was weakly but significantly (p < 0.05) and inversely correlated with cognitive decline. Conclusion: Fibrinogen isoforms may play important roles in the vascular pathology of AD as well as neuroinflammation. As such, fibrinogen appears to be a promising blood-based biomarker for AD. Further validation of the present findings in larger population is now warranted.
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Affiliation(s)
- Siti Hajar Rehiman
- Collaborative Drug Discovery Research (CDDR) and Brain Degeneration and Therapeutics Research Group, Faculty of Pharmacy, University Teknologi MARA (UiTM) Cawangan Selangor, Bandar Puncak Alam, Selangor Darul Ehsan, Malaysia
| | - Siong Meng Lim
- Collaborative Drug Discovery Research (CDDR) and Brain Degeneration and Therapeutics Research Group, Faculty of Pharmacy, University Teknologi MARA (UiTM) Cawangan Selangor, Bandar Puncak Alam, Selangor Darul Ehsan, Malaysia
| | - Fei Tieng Lim
- Collaborative Drug Discovery Research (CDDR) and Brain Degeneration and Therapeutics Research Group, Faculty of Pharmacy, University Teknologi MARA (UiTM) Cawangan Selangor, Bandar Puncak Alam, Selangor Darul Ehsan, Malaysia
| | - Ai-Vyrn Chin
- Division of Geriatric Medicine, Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Maw Pin Tan
- Division of Geriatric Medicine, Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Shahrul Bahyah Kamaruzzaman
- Division of Geriatric Medicine, Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kalavathy Ramasamy
- Collaborative Drug Discovery Research (CDDR) and Brain Degeneration and Therapeutics Research Group, Faculty of Pharmacy, University Teknologi MARA (UiTM) Cawangan Selangor, Bandar Puncak Alam, Selangor Darul Ehsan, Malaysia
| | - Abu Bakar Abdul Majeed
- Collaborative Drug Discovery Research (CDDR) and Brain Degeneration and Therapeutics Research Group, Faculty of Pharmacy, University Teknologi MARA (UiTM) Cawangan Selangor, Bandar Puncak Alam, Selangor Darul Ehsan, Malaysia
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17
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Tang XM, Guo JL, Chen L, Ho PCL. Application for proteomics analysis technology in studying animal-derived traditional Chinese medicine: A review. J Pharm Biomed Anal 2020; 191:113609. [PMID: 32966940 DOI: 10.1016/j.jpba.2020.113609] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/28/2020] [Accepted: 08/29/2020] [Indexed: 10/23/2022]
Abstract
Different therapeutically active ingredients, from plants, animals, and mineral sources, are prescribed as traditional Chinese medicines (TCM). TCMs, from animal sources, are rich in proteins and peptides. Different advanced proteomics technologies, such as two-dimensional gel electrophoresis (2-DE), multi-dimensional liquid chromatography (MDLC), matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS), and isobaric tags for relative and absolute quantitation (iTRAQ), have been applied to analyze TCMs, from animal sources. This paper reviews the common proteomic techniques for analyzing animal - derived TCMs. Various scientific studies have reported the application of proteomics for locating drug targets, identifying active components, and elucidating the mechanisms of action of animal - derived TCMs. However, these researches are still at the preliminary stage. This review has also discussed the existing challenges and future directions in this field of research.
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Affiliation(s)
- Xue-Mei Tang
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jin-Lin Guo
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Lu Chen
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
| | - Paul Chi-Lui Ho
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117543, Singapore.
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18
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Cozzolino F, Landolfi A, Iacobucci I, Monaco V, Caterino M, Celentano S, Zuccato C, Cattaneo E, Monti M. New label-free methods for protein relative quantification applied to the investigation of an animal model of Huntington Disease. PLoS One 2020; 15:e0238037. [PMID: 32886703 PMCID: PMC7473538 DOI: 10.1371/journal.pone.0238037] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/07/2020] [Indexed: 12/27/2022] Open
Abstract
Spectral Counts approaches (SpCs) are largely employed for the comparison of protein expression profiles in label-free (LF) differential proteomics applications. Similarly, to other comparative methods, also SpCs based approaches require a normalization procedure before Fold Changes (FC) calculation. Here, we propose new Complexity Based Normalization (CBN) methods that introduced a variable adjustment factor (f), related to the complexity of the sample, both in terms of total number of identified proteins (CBN(P)) and as total number of spectral counts (CBN(S)). Both these new methods were compared with the Normalized Spectral Abundance Factor (NSAF) and the Spectral Counts log Ratio (Rsc), by using standard protein mixtures. Finally, to test the robustness and the effectiveness of the CBNs methods, they were employed for the comparative analysis of cortical protein extract from zQ175 mouse brains, model of Huntington Disease (HD), and control animals (raw data available via ProteomeXchange with identifier PXD017471). LF data were also validated by western blot and MRM based experiments. On standard mixtures, both CBN methods showed an excellent behavior in terms of reproducibility and coefficients of variation (CVs) in comparison to the other SpCs approaches. Overall, the CBN(P) method was demonstrated to be the most reliable and sensitive in detecting small differences in protein amounts when applied to biological samples.
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Affiliation(s)
- Flora Cozzolino
- Department of Chemical Sciences, University of Naples "Federico II", Naples, Italy
- CEINGE Advanced Biotechnologies, Naples, Italy
| | - Alfredo Landolfi
- Department of Chemical Sciences, University of Naples "Federico II", Naples, Italy
- CEINGE Advanced Biotechnologies, Naples, Italy
| | - Ilaria Iacobucci
- Department of Chemical Sciences, University of Naples "Federico II", Naples, Italy
- CEINGE Advanced Biotechnologies, Naples, Italy
| | | | - Marianna Caterino
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Naples, Italy
| | | | - Chiara Zuccato
- Department of Biosciences, University of Milan, Milan, Italy
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Elena Cattaneo
- Department of Biosciences, University of Milan, Milan, Italy
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Maria Monti
- Department of Chemical Sciences, University of Naples "Federico II", Naples, Italy
- CEINGE Advanced Biotechnologies, Naples, Italy
- * E-mail:
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19
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Wu X, Luo L, Kong R, Song Y, Li Q, Nice EC, Wang K. Recent advances in autophagic machinery: a proteomic perspective. Expert Rev Proteomics 2020; 17:561-579. [PMID: 32772586 DOI: 10.1080/14789450.2020.1808464] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Autophagy is an evolutionarily conserved cellular clearance process, by which cytosolic components are delivered to autolysosomes for breakdown and recycling to maintain cellular homeostasis. During the past decades, autophagy has been found to be tightly implicated in various physiological and pathological progresses. Unraveling the regulatory mechanisms of the autophagy process will contribute to the development of emerging autophagy-targeting strategies for the treatment of various diseases. Recently, the rapid development of proteomics approaches has enabled the use of large-scale unbiased strategies to unravel autophagy machinery. AREAS COVERED In this review, we will highlight the recent contributions of proteomics strategies in clarifying the autophagy machinery, with an emphasis on the three different types of autophagy (namely macroautophagy, microautophagy, and chaperone-mediated autophagy). We will also discuss the emerging role of proteomics approaches in investigating the mechanism of the autophagy-based unconventional secretory pathway (secretory autophagy). EXPERT OPINION Proteomics has provided an effective strategy for the comprehensive analysis of the autophagy process, which will broaden our understanding of autophagy machinery, and holds great promise for developing clinical therapies targeting autophagy.
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Affiliation(s)
- Xingyun Wu
- West China School of Basic Medical Sciences & Forensic Medicine, Center of Reproductive Medicine, West China Second University Hospital, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu, P.R. China
| | - Li Luo
- West China School of Basic Medical Sciences & Forensic Medicine, Center of Reproductive Medicine, West China Second University Hospital, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu, P.R. China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education , Chengdu, P.R. China
| | - Ruxin Kong
- West China School of Basic Medical Sciences & Forensic Medicine, Center of Reproductive Medicine, West China Second University Hospital, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu, P.R. China
| | - Yabing Song
- West China School of Basic Medical Sciences & Forensic Medicine, Center of Reproductive Medicine, West China Second University Hospital, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu, P.R. China
| | - Qifu Li
- Department of Neurology, the First Affiliated Hospital of Hainan Medical University, and Key Laboratory of Brain Science Research & Transformation in Tropical Environment of Hainan Province, Hainan Medical University , Haikou, P.R. China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University , Clayton, Australia
| | - Kui Wang
- West China School of Basic Medical Sciences & Forensic Medicine, Center of Reproductive Medicine, West China Second University Hospital, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu, P.R. China
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20
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Proteomic analysis of Antrodia Cinnamomea-induced ER stress in liver cancer cells. J Pharm Biomed Anal 2020; 187:113142. [PMID: 32460214 DOI: 10.1016/j.jpba.2020.113142] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/25/2020] [Accepted: 02/01/2020] [Indexed: 01/01/2023]
Abstract
Antrodia Cinnamomea is a fungus species widely used as a herb medicine for hypertension, cancer and handover. Nevertheless, the biological roles of Antrodia Cinnamomea on the molecular mechanism of liver cancer are not entirely understood. To determine whether Antrodia Cinnamomea is able to be used for the treatment of liver cancer and its molecular mechanism, we examined the effect of Antrodia Cinnamomea on the differential proteomic patterns in liver cancer cell lines HepG2 and C3A as well as in Chang's liver cell, a normal liver cell, using quantitative proteomic approach. The proteomic analysis demonstrated that abundance of 82, 125 and 125 proteins was significantly altered in Chang's liver cells, C3A and HepG2, respectively. The experimental outcomes also demonstrated that Antrodia Cinnamomea-induced cytotoxicity in liver cancer cells mostly involved dysregulation of protein folding, cytoskeleton regulation, redox-regulation, glycolysis pathway as well as transcription regulation. Further analysis also revealed that Antrodia Cinnamomea promoted misfolding of intracellular proteins and dysregulate of cellular redox-balance resulting in ER-stress. To sum up our studies demonstrated that the proteomic strategy used in this study offered a tool to investigate the molecular mechanisms of Antrodia Cinnamomea-induced liver cancer cytotoxicity. The proteomic results might be further evaluated as prospective targets in liver cancer treatment.
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21
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García-Estrada C, Martín JF, Cueto L, Barreiro C. Omics Approaches Applied to Penicillium chrysogenum and Penicillin Production: Revealing the Secrets of Improved Productivity. Genes (Basel) 2020; 11:genes11060712. [PMID: 32604893 PMCID: PMC7348727 DOI: 10.3390/genes11060712] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/07/2020] [Accepted: 06/24/2020] [Indexed: 12/20/2022] Open
Abstract
Penicillin biosynthesis by Penicillium chrysogenum is one of the best-characterized biological processes from the genetic, molecular, biochemical, and subcellular points of view. Several omics studies have been carried out in this filamentous fungus during the last decade, which have contributed to gathering a deep knowledge about the molecular mechanisms underlying improved productivity in industrial strains. The information provided by these studies is extremely useful for enhancing the production of penicillin or other bioactive secondary metabolites by means of Biotechnology or Synthetic Biology.
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Affiliation(s)
- Carlos García-Estrada
- INBIOTEC (Instituto de Biotecnología de León). Avda. Real 1—Parque Científico de León, 24006 León, Spain; (L.C.); (C.B.)
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
- Correspondence: or ; Tel.: +34-987210308
| | - Juan F. Martín
- Área de Microbiología, Departamento de Biología Molecular, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain;
| | - Laura Cueto
- INBIOTEC (Instituto de Biotecnología de León). Avda. Real 1—Parque Científico de León, 24006 León, Spain; (L.C.); (C.B.)
| | - Carlos Barreiro
- INBIOTEC (Instituto de Biotecnología de León). Avda. Real 1—Parque Científico de León, 24006 León, Spain; (L.C.); (C.B.)
- Departamento de Biología Molecular, Universidad de León, Campus de Ponferrada, Avda. Astorga s/n, 24401 Ponferrada, Spain
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22
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Dowling P, Zweyer M, Swandulla D, Ohlendieck K. Characterization of Contractile Proteins from Skeletal Muscle Using Gel-Based Top-Down Proteomics. Proteomes 2019; 7:proteomes7020025. [PMID: 31226838 PMCID: PMC6631179 DOI: 10.3390/proteomes7020025] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 12/22/2022] Open
Abstract
The mass spectrometric analysis of skeletal muscle proteins has used both peptide-centric and protein-focused approaches. The term 'top-down proteomics' is often used in relation to studying purified proteoforms and their post-translational modifications. Two-dimensional gel electrophoresis, in combination with peptide generation for the identification and characterization of intact proteoforms being present in two-dimensional spots, plays a critical role in specific applications of top-down proteomics. A decisive bioanalytical advantage of gel-based and top-down approaches is the initial bioanalytical focus on intact proteins, which usually enables the swift identification and detailed characterisation of specific proteoforms. In this review, we describe the usage of two-dimensional gel electrophoretic top-down proteomics and related approaches for the systematic analysis of key components of the contractile apparatus, with a special focus on myosin heavy and light chains and their associated regulatory proteins. The detailed biochemical analysis of proteins belonging to the thick and thin skeletal muscle filaments has decisively improved our biochemical understanding of structure-function relationships within the contractile apparatus. Gel-based and top-down proteomics has clearly established a variety of slow and fast isoforms of myosin, troponin and tropomyosin as excellent markers of fibre type specification and dynamic muscle transition processes.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
- MU Human Health Research Institute, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
| | - Margit Zweyer
- Institute of Physiology II, University of Bonn, D-53115 Bonn, Germany.
| | - Dieter Swandulla
- Institute of Physiology II, University of Bonn, D-53115 Bonn, Germany.
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
- MU Human Health Research Institute, Maynooth University, Maynooth, W23F2H6 Co. Kildare, Ireland.
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23
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Barreiro C, García-Estrada C. Proteomics and Penicillium chrysogenum: Unveiling the secrets behind penicillin production. J Proteomics 2018; 198:119-131. [PMID: 30414515 DOI: 10.1016/j.jprot.2018.11.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 10/27/2018] [Accepted: 11/05/2018] [Indexed: 01/29/2023]
Abstract
Discovery, industrial production and clinical applications of penicillin, together with scientific findings on penicillin biosynthesis and its complex regulation, are model milestones of the historical evolution of the most recognized 'magic bullet' against microbial infections available in the worldwide market. Thousands of tons of penicillin produced nowadays are the result of a huge number of technical, industrial and scientific tackled and solved challenges. This combination of, sometimes unsuspected, findings has given Proteomics the chance to support the understanding of the physiology of the high-producing fungal strains and the development of enhanced mutants by means of inverse engineering. Thus, this review, which is part of the special issue entitled "A Tribute to J. Proteomics on its 10th Anniversary", describes how Proteomics has contributed to characterize different aspects related to penicillin production in Penicillium chrosogenum. It covers from global proteome characterizations (intracellular, extracellular and microbodies) to proteome-wide comparative analyses between different penicillin-producing mutant strains and conditions, paying special attention to the methodologies used, as well as to the most important outcomes. As a result, a guide of Proteomics approaches applied to the characterization of penicillin production by P. chrysogenum is detailed in the birthday of the Fleming's most relevant finding. SIGNIFICANCE: Although the discovery of penicillin is celebrating the 90th birthday and its clinical application is worldwide recognized, in fact, semisynthetic penicillins are still one of the most prescribed antibiotics, only the arrival of the post-genomic era during the first decade of the 21st century, and more precisely the Proteomics approaches, have contributed to unveil the industrial secrets behind penicillin production. This review provides relevant information, based on proteomics studies, about the molecular mechanisms responsible for increased penicillin titres, and therefore, may represent a clear model of inverse engineering in microorganisms.
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Affiliation(s)
- Carlos Barreiro
- INBIOTEC (Instituto de Biotecnología de León), Avda. Real 1 - Parque Científico de León, 24006 León, Spain; Departamento de Biología Molecular, Universidad de León, Campus de Ponferrada, Avda. Astorga s/n, 24401 Ponferrada, Spain.
| | - Carlos García-Estrada
- INBIOTEC (Instituto de Biotecnología de León), Avda. Real 1 - Parque Científico de León, 24006 León, Spain; Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
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24
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Lau BYC, Othman A, Ramli US. Application of Proteomics Technologies in Oil Palm Research. Protein J 2018; 37:473-499. [DOI: 10.1007/s10930-018-9802-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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25
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Bonar EA, Bukowski M, Hydzik M, Jankowska U, Kedracka-Krok S, Groborz M, Dubin G, Akkerboom V, Miedzobrodzki J, Sabat AJ, Friedrich AW, Wladyka B. Joint Genomic and Proteomic Analysis Identifies Meta-Trait Characteristics of Virulent and Non-virulent Staphylococcus aureus Strains. Front Cell Infect Microbiol 2018; 8:313. [PMID: 30237986 PMCID: PMC6136393 DOI: 10.3389/fcimb.2018.00313] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/16/2018] [Indexed: 12/18/2022] Open
Abstract
Staphylococcus aureus is an opportunistic pathogen of humans and warm-blooded animals and presents a growing threat in terms of multi-drug resistance. Despite numerous studies, the basis of staphylococcal virulence and switching between commensal and pathogenic phenotypes is not fully understood. Using genomics, we show here that S. aureus strains exhibiting virulent (VIR) and non-virulent (NVIR) phenotypes in a chicken embryo infection model genetically fall into two separate groups, with the VIR group being much more cohesive than the NVIR group. Significantly, the genes encoding known staphylococcal virulence factors, such as clumping factors, are either found in different allelic variants in the genomes of NVIR strains (compared to VIR strains) or are inactive pseudogenes. Moreover, the pyruvate carboxylase and gamma-aminobutyrate permease genes, which were previously linked with virulence, are pseudogenized in NVIR strain ch22. Further, we use comprehensive proteomics tools to characterize strains that show opposing phenotypes in a chicken embryo virulence model. VIR strain CH21 had an elevated level of diapolycopene oxygenase involved in staphyloxanthin production (protection against free radicals) and expressed a higher level of immunoglobulin-binding protein Sbi on its surface compared to NVIR strain ch22. Furthermore, joint genomic and proteomic approaches linked the elevated production of superoxide dismutase and DNA-binding protein by NVIR strain ch22 with gene duplications.
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Affiliation(s)
- Emilia A Bonar
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Michal Bukowski
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Marcin Hydzik
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Urszula Jankowska
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Sylwia Kedracka-Krok
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Magdalena Groborz
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Viktoria Akkerboom
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Jacek Miedzobrodzki
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Artur J Sabat
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Alexander W Friedrich
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Benedykt Wladyka
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
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26
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Gel-based proteomics in disease research: Is it still valuable? BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:9-16. [PMID: 30392562 DOI: 10.1016/j.bbapap.2018.08.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 06/30/2018] [Accepted: 08/09/2018] [Indexed: 12/17/2022]
Abstract
Gel electrophoresis had been the primary method in proteomics. In the early era of proteomics, gel electrophoresis was a dominant technique of sample preparation for mass spectrometry analysis. Particularly, two-dimensional electrophoresis provided high-resolution proteome separation, and was regarded as the standard methodology for the separation of wide-range proteomes. However, gel electrophoresis turned downwards due to the progress of other separations including liquid chromatography and ionization techniques, resulting gel-free proteomics finally becoming dominant players at present. There are numerous advantages in gel-free approach in aspects of current trends of disease research. Interestingly, gel-free approaches are still advanced, it seems that gel electrophoresis will not be disappeared. The unique features of gel electrophoresis can be complementary for gel-free and it is suitable for the new wave of top-down functional proteomics.
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Yu HI, Chou HC, Su YC, Lin LH, Lu CH, Chuang HH, Tsai YT, Liao EC, Wei YS, Yang YT, Lee YR, Chan HL. Proteomic analysis of evodiamine-induced cytotoxicity in thyroid cancer cells. J Pharm Biomed Anal 2018; 160:344-350. [PMID: 30114613 DOI: 10.1016/j.jpba.2018.08.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 07/27/2018] [Accepted: 08/04/2018] [Indexed: 01/07/2023]
Abstract
Evodiamine is a natural product extracted from herbal plants such as Tetradium which has shown to have anti-fat uptake and anti-proliferation properties. However, the effects of evodiamine on the behavior of thyroid cancers are largely unknown. To determine if evodiamine might be useful in the treatment of thyroid cancer and its cytotoxic mechanism, we analyzed the impact of evodiamine treatment on differential protein expression in human thyroid cancer cell line ARO using lysine-labeling two-dimensional difference gel electrophoresis (2D-DIGE) combined with mass spectrometry (MS). This study demonstrated 77 protein features that were significantly changed in protein expression and revealed evodiamine-induced cytotoxicity in thyroid cancer cells involves dysregulation of protein folding, cytoskeleton, cytoskeleton regulation and transcription control. Our work shows that this combined proteomic strategy provides a rapid method to study the molecular mechanisms of evodiamine-induced cytotoxicity in thyroid cancer cells. The identified targets may be useful for further evaluation as potential targets in thyroid cancer therapy.
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Affiliation(s)
- Hui-I Yu
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi, Taiwan
| | - Hsiu-Chuan Chou
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Yi-Ching Su
- Department of Applied Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Li-Hsun Lin
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Chieh-Hsiang Lu
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi, Taiwan
| | - Hsiang-Hsun Chuang
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi, Taiwan
| | - Yi-Ting Tsai
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu 300, Taiwan
| | - En-Chi Liao
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Yu-Shan Wei
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Yi-Ting Yang
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Ying-Ray Lee
- Department of Medical Research, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi, Taiwan.
| | - Hong-Lin Chan
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu 300, Taiwan.
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Proteomic analysis of honokiol-induced cytotoxicity in thyroid cancer cells. Life Sci 2018; 207:184-204. [PMID: 29883720 DOI: 10.1016/j.lfs.2018.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 05/24/2018] [Accepted: 06/02/2018] [Indexed: 12/16/2022]
Abstract
AIMS Honokiol is a natural product extracted from herbal plants such as the Magnolia species which have been shown to exhibit anti-tumor and anti-metastatic properties. However, the effects of honokiol on thyroid cancers are largely unknown. MATERIALS AND METHODS To determine whether honokiol might be useful for the treatment of thyroid cancer and to elucidate the mechanism of toxicity of honokiol, we analyzed the impact of honokiol treatment on differential protein expression in human thyroid cancer cell line ARO using lysine-labeling two-dimensional difference gel electrophoresis (2D-DIGE) combined with mass spectrometry (MS). KEY FINDINGS This study revealed 178 proteins that showed a significant change in expression levels and also revealed that honokiol-induced cytotoxicity in thyroid cancer cells involves dysregulation of cytoskeleton, protein folding, transcription control and glycolysis. SIGNIFICANCE Our work shows that combined proteomic strategy provides a rapid method to study the molecular mechanisms of honokiol-induced cytotoxicity in thyroid cancer cells. The identified targets may be useful for further evaluation as potential targets in thyroid cancer therapy.
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Bashizadeh Fakhar H, Rezaie-Tavirani M, Zali H, Darkhaneh RF, Nejad EK, Aghazadeh MH. Proteomic Analysis of Low-Grade Serous Ovarian Cancer and Comparing It with Non-cancerous Ovarian. INDIAN JOURNAL OF GYNECOLOGIC ONCOLOGY 2018. [DOI: 10.1007/s40944-018-0187-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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30
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Sawicki LA, Choe LH, Wiley KL, Lee KH, Kloxin AM. Isolation and Identification of Proteins Secreted by Cells Cultured within Synthetic Hydrogel-Based Matrices. ACS Biomater Sci Eng 2018; 4:836-845. [PMID: 29552635 PMCID: PMC5850091 DOI: 10.1021/acsbiomaterials.7b00647] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 02/02/2018] [Indexed: 01/14/2023]
Abstract
Cells interact with and remodel their microenvironment, degrading large extracellular matrix (ECM) proteins (e.g., fibronectin, collagens) and secreting new ECM proteins and small soluble factors (e.g., growth factors, cytokines). Synthetic mimics of the ECM have been developed as controlled cell culture platforms for use in both fundamental and applied studies. However, how cells broadly remodel these initially well-defined matrices remains poorly understood and difficult to probe. In this work, we have established methods for widely examining both large and small proteins that are secreted by cells within synthetic matrices. Specifically, human mesenchymal stem cells (hMSCs), a model primary cell type, were cultured within well-defined poly(ethylene glycol) (PEG)-peptide hydrogels, and these cell-matrix constructs were decellularized and degraded for subsequent isolation and analysis of deposited proteins. Shotgun proteomics using liquid chromatography and mass spectrometry identified a variety of proteins, including the large ECM proteins fibronectin and collagen VI. Immunostaining and confocal imaging confirmed these results and provided visualization of protein organization within the synthetic matrices. Additionally, culture medium was collected from the encapsulated hMSCs, and a Luminex assay was performed to identify secreted soluble factors, including vascular endothelial growth factor (VEGF), endothelial growth factor (EGF), basic fibroblast growth factor (FGF-2), interleukin 8 (IL-8), and tumor necrosis factor alpha (TNF-α). Together, these methods provide a unique approach for studying dynamic reciprocity between cells and synthetic microenvironments and have the potential to provide new biological insights into cell responses during three-dimensional (3D) controlled cell culture.
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Affiliation(s)
- Lisa A. Sawicki
- Department
of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Leila H. Choe
- Department
of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
- Delaware
Biotechnology Institute, Newark, Delaware 19711, United States
| | - Katherine L. Wiley
- Department
of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Kelvin H. Lee
- Department
of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
- Delaware
Biotechnology Institute, Newark, Delaware 19711, United States
| | - April M. Kloxin
- Department
of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
- Department
of Materials Science and Engineering, University
of Delaware, Newark, Delaware 19716, United
States
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31
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Abstract
Gel-based proteomics has been widely used for the systematic cataloging of the protein constituents of defined biofluids, purified organelles, individual cell types, heterogeneous tissues and isolated organs, as well as being applied to comparative biochemical and biomedical analyses of complex biological specimens. Of the many electrophoretic techniques used in modern biochemical approaches, large-scale protein separation by difference gel electrophoresis (DIGE) has established itself as the most powerful analytical tool in comparative proteomics. Both 2-dye and 3-dye fluorescence systems with minimal or saturation labeling are routinely used. This chapter briefly describes the technical advantages of the pre-electrophoretic fluorescent labeling technique and discusses the bioanalytical usefulness of this highly successful electrophoretic method.
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Affiliation(s)
- Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
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32
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Abstract
The skeletal muscle proteome consists of a large number of diverse protein species with a broad and dynamic concentration range. Since mature skeletal muscles are characterized by a specific combination of contractile cells with differing physiological and biochemical properties, it is essential to determine specific differences in the protein composition of fast, slow, and hybrid fibers. Fluorescence two-dimensional gel electrophoresis (DIGE) is a powerful comparative tool to analyze fiber type-specific differences between fast and slow muscles. In this chapter, the application of the DIGE method for the comparative analysis of different subtypes of skeletal muscles is outlined in detail. A standardized proteomic workflow is described, involving sample preparation, protein extraction, differential fluorescence labeling using a 3-dye system, first-dimension isoelectric focusing, second-dimension slab gel electrophoresis, DIGE image analysis, protein digestion, and mass spectrometry.
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Affiliation(s)
- Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
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Liu XX, Ye H, Wang P, Zhang Y, Zhang JY. Identification of 14‑3‑3ζ as a potential biomarker in gastric cancer by proteomics‑based analysis. Mol Med Rep 2017; 16:7759-7765. [PMID: 28944820 DOI: 10.3892/mmr.2017.7496] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 07/20/2017] [Indexed: 11/06/2022] Open
Abstract
The identification of tumor biomarkers to support early diagnosis and tumor progression monitoring may potentially reduce the mortality of gastric cancer (GC). The present study aimed to detect novel tumor‑associated antigens from the AGS GC cell line, and to identify their associated autoantibodies in sera from patients with GC by proteomics‑based approaches. Proteins from AGS cell lysates were isolated using two‑dimensional polyacrylamide gel electrophoresis, and western blotting was subsequently performed, to determine autoantibody responses in sera derived from patients with GC and healthy individuals. Positive protein spots were removed from gels stained with Coomassie blue, and were then evaluated by liquid chromatography‑tandem mass spectrometry. Sera from patients with GC produced numerous spots, one of which was identified as 14‑3‑3ζ. Autoantibody frequency to 14‑3‑3ζ was 17.6% (15/85) in patients with GC, which was significantly higher than that in healthy control individuals (2.4%; 2/85; P<0.01). These results suggested that the autoantibody against 14‑3‑3ζ may be a potential serological biomarker for the detection and diagnosis of GC.
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Affiliation(s)
- Xin-Xin Liu
- Center for Tumor Biotherapy, The First Affiliated Hospital of Zhengzhou University and College of Public Health, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Hua Ye
- Center for Tumor Biotherapy, The First Affiliated Hospital of Zhengzhou University and College of Public Health, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Peng Wang
- Center for Tumor Biotherapy, The First Affiliated Hospital of Zhengzhou University and College of Public Health, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Yi Zhang
- Center for Tumor Biotherapy, The First Affiliated Hospital of Zhengzhou University and College of Public Health, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Jian-Ying Zhang
- Center for Tumor Biotherapy, The First Affiliated Hospital of Zhengzhou University and College of Public Health, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
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Nynca J, Arnold G, Fröhlich T, Ciereszko A. Proteomic identification of rainbow trout blood plasma proteins and their relationship to seminal plasma proteins. Proteomics 2017; 17. [DOI: 10.1002/pmic.201600460] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 03/31/2017] [Accepted: 04/07/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Joanna Nynca
- Department of Gametes and Embryo Biology; Institute of Animal Reproduction and Food Research; Polish Academy of Sciences; Olsztyn Poland
| | - Georg Arnold
- Laboratory for Functional Genome Analysis; Gene Center and Department of Biochemistry; Ludwig-Maximilians-Universität; Munich Germany
| | - Thomas Fröhlich
- Laboratory for Functional Genome Analysis; Gene Center and Department of Biochemistry; Ludwig-Maximilians-Universität; Munich Germany
| | - Andrzej Ciereszko
- Department of Gametes and Embryo Biology; Institute of Animal Reproduction and Food Research; Polish Academy of Sciences; Olsztyn Poland
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35
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Zhai Q, Xiao Y, Zhao J, Tian F, Zhang H, Narbad A, Chen W. Identification of key proteins and pathways in cadmium tolerance of Lactobacillus plantarum strains by proteomic analysis. Sci Rep 2017; 7:1182. [PMID: 28446769 PMCID: PMC5430759 DOI: 10.1038/s41598-017-01180-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 03/22/2017] [Indexed: 12/20/2022] Open
Abstract
Our previous study confirmed the protective potential of Lactobacillus plantarum (L. plantarum) strains in alleviation of cadmium (Cd) toxicity in vivo and demonstrated that the observed protection largely depended on the tolerance of the strains to Cd-induced stress. It was also observed that there were significant intra-species differences in Cd tolerance of L. plantarum strains. In this study, we investigated the mechanism of Cd induced stress response of L. plantarum strains using the isobaric tags for relative and absolute quantitation (iTRAQ) based comparative proteomics. L. plantarum CCFM8610 (strongly resistant to Cd) and L. plantarum CCFM191 (sensitive to Cd) were selected as target strains, and their proteomic profiles in the presence and absence of Cd exposure were compared. We propose that the underlying mechanism of the exceptional Cd tolerance of CCFM8610 may be attributed to the following: (a) a specific energy-conservation survival mode; (b) mild induction of its cellular defense and repair system; (c) an enhanced biosynthesis of hydrophobic amino acids in response to Cd; (d) inherent superior Cd binding ability and effective cell wall biosynthesis ability; (e) a tight regulation on ion transport; (f) several key proteins, including prophage P2b protein 18, CadA, mntA and lp_3327.
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Affiliation(s)
- Qixiao Zhai
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, People's Republic of China.,UK-China Joint Centre on Probiotic Bacteria, Norwich, NR4 7UA, UK
| | - Yue Xiao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, People's Republic of China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, People's Republic of China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, People's Republic of China.,UK-China Joint Centre on Probiotic Bacteria, Norwich, NR4 7UA, UK
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, People's Republic of China.,UK-China Joint Centre on Probiotic Bacteria, Norwich, NR4 7UA, UK
| | - Arjan Narbad
- UK-China Joint Centre on Probiotic Bacteria, Norwich, NR4 7UA, UK.,Gut Health and Food Safety Programme, Institute of Food Research, Norwich, NR4 7UA, United Kingdom
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, People's Republic of China. .,UK-China Joint Centre on Probiotic Bacteria, Norwich, NR4 7UA, UK. .,Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology & Business University, Beijing, 100048, People's Republic of China.
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36
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Jin P, Wang K, Huang C, Nice EC. Mining the fecal proteome: from biomarkers to personalised medicine. Expert Rev Proteomics 2017; 14:445-459. [PMID: 28361558 DOI: 10.1080/14789450.2017.1314786] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Fecal proteomics has gained increased prominence in recent years. It can provide insights into the diagnosis and surveillance of many bowel diseases by both identifying potential biomarkers in stool samples and helping identify disease-related pathways. Fecal proteomics has already shown its potential for the discovery and validation of biomarkers for colorectal cancer screening, and the analysis of fecal microbiota by MALDI-MS for the diagnosis of a range of bowel diseases is gaining clinical acceptance. Areas covered: Based on a comprehensive analysis of the current literature, we introduce the range of sensitive and specific proteomics methods which comprise the current 'Proteomics Toolbox', explain how the integration of fecal proteomics with data processing/bioinformatics has been used for the identification of potential biomarkers for both CRC and other gut-related pathologies and analysis of the fecal microbiome, outline some of the current fecal assays in current clinical practice and introduce the concept of personalised medicine which these technologies will help inform. Expert commentary: Integration of fecal proteomics with other proteomics and genomics strategies as well as bioinformatics is paving the way towards personalised medicine, which will bring with it improved global healthcare.
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Affiliation(s)
- Ping Jin
- a Key Laboratory of Tropical Diseases and Translational Medicine of Ministry of Education & Department of Neurology , the Affiliated Hospital of Hainan Medical College , Haikou , China.,b State Key Laboratory of Biotherapy and Cancer Center , West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China
| | - Kui Wang
- b State Key Laboratory of Biotherapy and Cancer Center , West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China
| | - Canhua Huang
- a Key Laboratory of Tropical Diseases and Translational Medicine of Ministry of Education & Department of Neurology , the Affiliated Hospital of Hainan Medical College , Haikou , China.,b State Key Laboratory of Biotherapy and Cancer Center , West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China
| | - Edouard C Nice
- b State Key Laboratory of Biotherapy and Cancer Center , West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China.,c Department of Biochemistry and Molecular Biology , Monash University , Clayton , Australia
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37
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Chen HY, Chou HC, Chang SJ, Liao EC, Tsai YT, Wei YS, Li JM, Lin LH, Lin MW, Chen YJ, Chen YS, Lin CC, Wang YS, Ko ML, Chan HL. Proteomic Analysis of Various Rat Ocular Tissues after Ischemia-Reperfusion Injury and Possible Relevance to Acute Glaucoma. Int J Mol Sci 2017; 18:ijms18020334. [PMID: 28165428 PMCID: PMC5343869 DOI: 10.3390/ijms18020334] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/26/2017] [Accepted: 01/26/2017] [Indexed: 12/21/2022] Open
Abstract
Glaucoma is a group of eye diseases that can cause vision loss and optical nerve damage. To investigate the protein expression alterations in various intraocular tissues (i.e., the cornea, conjunctiva, uvea, retina, and sclera) during ischemia–reperfusion (IR) injury, this study performed a proteomic analysis to qualitatively investigate such alterations resulting from acute glaucoma. The IR injury model combined with the proteomic analysis approach of two-dimensional difference gel electrophoresis (2D-DIGE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used to monitor the protein expression alterations in two groups of specimens (an IR injury group and a control group). The analysis results revealed 221 unique differentially expressed proteins of a total of 1481 proteins in the cornea between the two groups. In addition, 97 of 1206 conjunctival proteins, 90 of 1354 uveal proteins, 61 of 1180 scleral proteins, and 37 of 1204 retinal proteins were differentially expressed. These findings imply that different ocular tissues have different tolerances against IR injury. To sum up, this study utilized the acute glaucoma model combined with 2D-DIGE and MALDI-TOF MS to investigate the IR injury affected protein expression on various ocular tissues, and based on the ratio of protein expression alterations, the alterations in the ocular tissues were in the following order: the cornea, conjunctiva, uvea, sclera, and retina.
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Affiliation(s)
- Hsin-Yi Chen
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu 300, Taiwan.
| | - Hsiu-Chuan Chou
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu 300, Taiwan.
- Center for Teacher Education, National Tsing Hua University, Hsinchu 300, Taiwan.
- Department of Applied Science, National Hsinchu University of Education, Hsinchu 300, Taiwan.
| | - Shing-Jyh Chang
- Gynecologic Oncology Section Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu 300, Taiwan.
| | - En-Chi Liao
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu 300, Taiwan.
| | - Yi-Ting Tsai
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu 300, Taiwan.
| | - Yu-Shan Wei
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu 300, Taiwan.
| | - Ji-Min Li
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu 300, Taiwan.
| | - Li-Hsun Lin
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu 300, Taiwan.
| | - Meng-Wei Lin
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu 300, Taiwan.
| | - Ying-Jen Chen
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu 300, Taiwan.
| | - Yu-Sheng Chen
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu 300, Taiwan.
| | - Chih-Chun Lin
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu 300, Taiwan.
| | - Yi-Shiuan Wang
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu 300, Taiwan.
| | - Mei-Lan Ko
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu 300, Taiwan.
- Department of Ophthalmology, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu 300, Taiwan.
| | - Hong-Lin Chan
- Institute of Bioinformatics and Structural Biology & Department of Medical Sciences, National Tsing Hua University, Hsinchu 300, Taiwan.
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38
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Pérez V, López D, Boixadera E, Ibernón M, Espinal A, Bonet J, Romero R. Comparative differential proteomic analysis of minimal change disease and focal segmental glomerulosclerosis. BMC Nephrol 2017; 18:49. [PMID: 28158993 PMCID: PMC5291957 DOI: 10.1186/s12882-017-0452-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 01/16/2017] [Indexed: 01/18/2023] Open
Abstract
Background Minimal change disease (MCD) and primary focal segmental glomerulosclerosis (FSGS) are glomerular diseases characterized by nephrotic syndrome. Their diagnosis requires a renal biopsy, but it is an invasive procedure with potential complications. In a small biopsy sample, where only normal glomeruli are observed, FSGS cannot be differentiated from MCD. The correct diagnosis is crucial to an effective treatment, as MCD is normally responsive to steroid therapy, whereas FSGS is usually resistant. The purpose of our study was to discover and validate novel early urinary biomarkers capable to differentiate between MCD and FSGS. Methods Forty-nine patients biopsy-diagnosed of MCD and primary FSGS were randomly subdivided into a training set (10 MCD, 11 FSGS) and a validation set (14 MCD, 14 FSGS). The urinary proteome of the training set was analyzed by two-dimensional differential gel electrophoresis coupled with mass spectrometry. The proteins identified were quantified by enzyme-linked immunosorbent assay in urine samples from the validation set. Results Urinary concentration of alpha-1 antitrypsin, transferrin, histatin-3 and 39S ribosomal protein L17 was decreased and calretinin was increased in FSGS compared to MCD. These proteins were used to build a decision tree capable to predict patient’s pathology. Conclusions This preliminary study suggests a group of urinary proteins as possible non-invasive biomarkers with potential value in the differential diagnosis of MCD and FSGS. These biomarkers would reduce the number of misdiagnoses, avoiding unnecessary or inadequate treatments. Electronic supplementary material The online version of this article (doi:10.1186/s12882-017-0452-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vanessa Pérez
- Laboratory of Experimental Nephrology, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain. .,Department of Nephrology, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, ES-08916, Badalona, Barcelona, Spain.
| | - Dolores López
- Department of Pathology, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Ester Boixadera
- Applied Statistics Service, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Meritxell Ibernón
- Department of Nephrology, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, ES-08916, Badalona, Barcelona, Spain
| | - Anna Espinal
- Applied Statistics Service, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Josep Bonet
- Department of Nephrology, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, ES-08916, Badalona, Barcelona, Spain
| | - Ramón Romero
- Laboratory of Experimental Nephrology, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.,Department of Nephrology, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Carretera del Canyet s/n, ES-08916, Badalona, Barcelona, Spain.,Department of Medicine, Universitat Autònoma de Barcelona, Badalona, Spain
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39
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Josić D, Peršurić Ž, Rešetar D, Martinović T, Saftić L, Kraljević Pavelić S. Use of Foodomics for Control of Food Processing and Assessing of Food Safety. ADVANCES IN FOOD AND NUTRITION RESEARCH 2017; 81:187-229. [PMID: 28317605 DOI: 10.1016/bs.afnr.2016.12.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Food chain, food safety, and food-processing sectors face new challenges due to globalization of food chain and changes in the modern consumer preferences. In addition, gradually increasing microbial resistance, changes in climate, and human errors in food handling remain a pending barrier for the efficient global food safety management. Consequently, a need for development, validation, and implementation of rapid, sensitive, and accurate methods for assessment of food safety often termed as foodomics methods is required. Even though, the growing role of these high-throughput foodomic methods based on genomic, transcriptomic, proteomic, and metabolomic techniques has yet to be completely acknowledged by the regulatory agencies and bodies. The sensitivity and accuracy of these methods are superior to previously used standard analytical procedures and new methods are suitable to address a number of novel requirements posed by the food production sector and global food market.
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Affiliation(s)
- D Josić
- University of Rijeka, Centre for High-Throughput Technologies, Radmile Matejčić 2, Rijeka, Croatia.
| | - Ž Peršurić
- University of Rijeka, Centre for High-Throughput Technologies, Radmile Matejčić 2, Rijeka, Croatia
| | - D Rešetar
- University of Rijeka, Centre for High-Throughput Technologies, Radmile Matejčić 2, Rijeka, Croatia
| | - T Martinović
- University of Rijeka, Centre for High-Throughput Technologies, Radmile Matejčić 2, Rijeka, Croatia
| | - L Saftić
- University of Rijeka, Centre for High-Throughput Technologies, Radmile Matejčić 2, Rijeka, Croatia
| | - S Kraljević Pavelić
- University of Rijeka, Centre for High-Throughput Technologies, Radmile Matejčić 2, Rijeka, Croatia
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40
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Zhou L, Wen J, Huang Z, Nice EC, Huang C, Zhang H, Li Q. Redox proteomics screening cellular factors associated with oxidative stress in hepatocarcinogenesis. Proteomics Clin Appl 2016; 11. [PMID: 27763721 DOI: 10.1002/prca.201600089] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 10/10/2016] [Accepted: 10/18/2016] [Indexed: 02/05/2023]
Abstract
Liver cancer is a major global health problem being the sixth most common cancer and the third cause of cancer-related death, with hepatocellular carcinoma (HCC) representing more than 90% of primary liver cancers. Mounting evidence suggests that, compared with their normal counterparts, many types of cancer cell have increased levels of ROS. Therefore, cancer cells need to combat high levels of ROS, especially at early stages of tumor development. Recent studies have revealed that ROS-mediated regulation of redox-sensitive proteins (redox sensors) is involved in the pathogenesis and/or progression of many human diseases, including cancer. Unraveling the altered functions of redox sensors and the underlying mechanisms in hepatocarcinogenesis is critical for the development of novel cancer therapeutics. For this reason, redox proteomics has been developed for the high-throughput screening of redox sensors, which will benefit the development of novel therapeutic strategies for the treatment of HCC. In this review, we will briefly introduce several novel redox proteomics techniques that are currently available to study various oxidative modifications in hepatocarcinogenesis and summarize the most important discoveries in the study of redox processes related to the development and progression of HCC.
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Affiliation(s)
- Li Zhou
- Key Laboratory of Tropical Diseases and Translational Medicine of Ministry of Education & Department of Neurology, the First Affiliated Hospital of Hainan Medical University, Haikou, P. R. China.,State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China
| | - Ji Wen
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Zhao Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia.,Visiting professor, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China
| | - Haiyuan Zhang
- Key Laboratory of Tropical Diseases and Translational Medicine of Ministry of Education & Department of Neurology, the First Affiliated Hospital of Hainan Medical University, Haikou, P. R. China
| | - Qifu Li
- Key Laboratory of Tropical Diseases and Translational Medicine of Ministry of Education & Department of Neurology, the First Affiliated Hospital of Hainan Medical University, Haikou, P. R. China
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41
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Staal JA, Pei Y, Rood BR. A Proteogenomic Approach to Understanding MYC Function in Metastatic Medulloblastoma Tumors. Int J Mol Sci 2016; 17:ijms17101744. [PMID: 27775567 PMCID: PMC5085772 DOI: 10.3390/ijms17101744] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/23/2016] [Accepted: 10/10/2016] [Indexed: 12/31/2022] Open
Abstract
Brain tumors are the leading cause of cancer-related deaths in children, and medulloblastoma is the most prevalent malignant childhood/pediatric brain tumor. Providing effective treatment for these cancers, with minimal damage to the still-developing brain, remains one of the greatest challenges faced by clinicians. Understanding the diverse events driving tumor formation, maintenance, progression, and recurrence is necessary for identifying novel targeted therapeutics and improving survival of patients with this disease. Genomic copy number alteration data, together with clinical studies, identifies c-MYC amplification as an important risk factor associated with the most aggressive forms of medulloblastoma with marked metastatic potential. Yet despite this, very little is known regarding the impact of such genomic abnormalities upon the functional biology of the tumor cell. We discuss here how recent advances in quantitative proteomic techniques are now providing new insights into the functional biology of these aggressive tumors, as illustrated by the use of proteomics to bridge the gap between the genotype and phenotype in the case of c-MYC-amplified/associated medulloblastoma. These integrated proteogenomic approaches now provide a new platform for understanding cancer biology by providing a functional context to frame genomic abnormalities.
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Affiliation(s)
- Jerome A Staal
- Multiple Sclerosis Department, Florey Institute of Neuroscience and Mental Health, Melbourne, VIC 3052, Australia.
- Center for Cancer and Immunology Research, Children's National Medical Center, Washington, DC 20010, USA.
| | - Yanxin Pei
- Center for Cancer and Immunology Research, Children's National Medical Center, Washington, DC 20010, USA.
| | - Brian R Rood
- Center for Cancer and Immunology Research, Children's National Medical Center, Washington, DC 20010, USA.
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42
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Murphy S, Dowling P, Ohlendieck K. Comparative Skeletal Muscle Proteomics Using Two-Dimensional Gel Electrophoresis. Proteomes 2016; 4:proteomes4030027. [PMID: 28248237 PMCID: PMC5217355 DOI: 10.3390/proteomes4030027] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/31/2016] [Accepted: 09/07/2016] [Indexed: 12/16/2022] Open
Abstract
The pioneering work by Patrick H. O’Farrell established two-dimensional gel electrophoresis as one of the most important high-resolution protein separation techniques of modern biochemistry (Journal of Biological Chemistry1975, 250, 4007–4021). The application of two-dimensional gel electrophoresis has played a key role in the systematic identification and detailed characterization of the protein constituents of skeletal muscles. Protein changes during myogenesis, muscle maturation, fibre type specification, physiological muscle adaptations and natural muscle aging were studied in depth by the original O’Farrell method or slightly modified gel electrophoretic techniques. Over the last 40 years, the combined usage of isoelectric focusing in the first dimension and sodium dodecyl sulfate polyacrylamide slab gel electrophoresis in the second dimension has been successfully employed in several hundred published studies on gel-based skeletal muscle biochemistry. This review focuses on normal and physiologically challenged skeletal muscle tissues and outlines key findings from mass spectrometry-based muscle proteomics, which was instrumental in the identification of several thousand individual protein isoforms following gel electrophoretic separation. These muscle-associated protein species belong to the diverse group of regulatory and contractile proteins of the acto-myosin apparatus that forms the sarcomere, cytoskeletal proteins, metabolic enzymes and transporters, signaling proteins, ion-handling proteins, molecular chaperones and extracellular matrix proteins.
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Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
| | - Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
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43
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Vellinger C, Sohm B, Parant M, Immel F, Usseglio-Polatera P. Investigating the emerging role of comparative proteomics in the search for new biomarkers of metal contamination under varying abiotic conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 562:974-986. [PMID: 27157531 DOI: 10.1016/j.scitotenv.2016.04.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 04/03/2016] [Accepted: 04/04/2016] [Indexed: 06/05/2023]
Abstract
This study aims at investigating the potential use of comparative proteomics as a multi-marker approach of metal contamination, taking into account the potential confounding effect of water temperature. The major objective was to identify combinations of proteins specifically responding to a given metal, even if included in a metal mixture. The diagnostic approach was performed via the comparative analysis of protein expression on spot mapping provided by adult males of Gammarus pulex (Amphipoda, Crustacea) respectively exposed to arsenate (As), cadmium (Cd) or a binary mixture of these metals (AsCd) at three realistic temperatures (5, 10 and 15°C). Proteomic expression analysis was performed by Differential in-Gel Electrophoresis (2D-DiGE), and completed by an adapted inferential statistical approach. Combinations of under/over-expressed protein spots discriminated the metal identity. However, none of these spots discriminated both the individual metal effect (As or Cd) and its effect in metal mixture (AsCd) whatever the tested temperature. Some limits of the two-dimensional analysis of protein spot maps in G. pulex have been highlighted: (i) the presence of contaminating peptides and/or abundant "déja-vu" proteins which can mask the responses of other proteins of interest or (ii) the presence of post-translational modifications. An optimization of the experimental design (especially during the sample preparation) has been described for future investigations. This study has also highlighted (i) the importance of precisely identifying the protein spots of interest to avoid erroneous interpretations in terms of action mechanisms of chemicals and (ii) the importance of working under controlled laboratory conditions with a temperature close to 10°C. In such conditions, we have demonstrated a higher impact of As than Cd on the energetic metabolism of Gammarus. This As impact is reduced in AsCd mixture confirming the antagonistic interaction of this binary mixture previously observed on G. pulex mortality at 10°C.
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Affiliation(s)
- Céline Vellinger
- Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), CNRS UMR 7360, Université de Lorraine - Metz, France.
| | - Bénédicte Sohm
- Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), CNRS UMR 7360, Université de Lorraine - Metz, France.
| | - Marc Parant
- Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), CNRS UMR 7360, Université de Lorraine - Metz, France.
| | - Françoise Immel
- Biogéosciences, CNRS UMR 6282, Université de Bourgogne - Dijon, France.
| | - Philippe Usseglio-Polatera
- Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), CNRS UMR 7360, Université de Lorraine - Metz, France.
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44
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Proteomic analysis of human tooth pulp proteomes – Comparison of caries-resistant and caries-susceptible persons. J Proteomics 2016; 145:127-136. [DOI: 10.1016/j.jprot.2016.04.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 04/08/2016] [Accepted: 04/17/2016] [Indexed: 01/13/2023]
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45
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Tonry CL, Leacy E, Raso C, Finn SP, Armstrong J, Pennington SR. The Role of Proteomics in Biomarker Development for Improved Patient Diagnosis and Clinical Decision Making in Prostate Cancer. Diagnostics (Basel) 2016; 6:E27. [PMID: 27438858 PMCID: PMC5039561 DOI: 10.3390/diagnostics6030027] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 06/28/2016] [Accepted: 07/07/2016] [Indexed: 02/06/2023] Open
Abstract
Prostate Cancer (PCa) is the second most commonly diagnosed cancer in men worldwide. Although increased expression of prostate-specific antigen (PSA) is an effective indicator for the recurrence of PCa, its intended use as a screening marker for PCa is of considerable controversy. Recent research efforts in the field of PCa biomarkers have focused on the identification of tissue and fluid-based biomarkers that would be better able to stratify those individuals diagnosed with PCa who (i) might best receive no treatment (active surveillance of the disease); (ii) would benefit from existing treatments; or (iii) those who are likely to succumb to disease recurrence and/or have aggressive disease. The growing demand for better prostate cancer biomarkers has coincided with the development of improved discovery and evaluation technologies for multiplexed measurement of proteins in bio-fluids and tissues. This review aims to (i) provide an overview of these technologies as well as describe some of the candidate PCa protein biomarkers that have been discovered using them; (ii) address some of the general limitations in the clinical evaluation and validation of protein biomarkers; and (iii) make recommendations for strategies that could be adopted to improve the successful development of protein biomarkers to deliver improvements in personalized PCa patient decision making.
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Affiliation(s)
- Claire L Tonry
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland.
| | - Emma Leacy
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland.
| | - Cinzia Raso
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland.
| | - Stephen P Finn
- School of Medicine, Trinity College Dublin, Dublin 2, Ireland.
| | | | - Stephen R Pennington
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland.
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46
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Yang H, Xu XL, Ma HM, Jiang J. Integrative analysis of transcriptomics and proteomics of skeletal muscles of the Chinese indigenous Shaziling pig compared with the Yorkshire breed. BMC Genet 2016; 17:80. [PMID: 27296698 PMCID: PMC4906580 DOI: 10.1186/s12863-016-0389-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 06/02/2016] [Indexed: 11/08/2022] Open
Abstract
Background The Shaziling pig (Sus scrofa) is a well-known indigenous breed in China. One of its main advantages over European breeds is its high meat quality. However, little genetic information is available for the Shaziling pig. To screen for differentially expressed genes and proteins that might be responsible for the meat quality, the longissimus dorsi muscles from Shaziling and Yorkshire pig breeds were investigated using an integrative analysis of transcriptomics and proteomics, involving high-throughput sequencing, the two-dimensional gel electrophoresis, and mass spectrometry. Results Sequencing produced 79,320 unigenes by de novo assembly, and 488 differentially expressed genes in the longissimus dorsi muscle of Shaziling pig compared with the Yorkshire breed were identified. Gene Ontology term enrichment of biological functions and Kyoto Encyclopedia of Genes and Genomes analysis showed that the gene products were mainly involved in metabolism, protein binding, and regulation of skeletal muscle development. At the protein level, 23 differentially expressed proteins were identified, which were potentially associated with fatty acid metabolism, the glycolytic pathway, and skeletal muscle growth. Eight differentially expressed genes were confirmed by real-time PCR. These results give an insight into the mechanisms underlying the formation of skeletal muscle in the Shaziling pig. Conclusions Certain differentially expressed genes and proteins are involved in fatty acid metabolism, intramuscular fat deposition, and skeletal muscle growth in the Shaziling pig. These results provide candidate genes for improving meat quality and will promote further transcriptomic research in Shaziling pigs. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0389-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hu Yang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, People's Republic of China.,College of Life Science and Resource Environment, Yichun University, Yichun, 336000, People's Republic of China
| | - Xing-Li Xu
- College of Life Science and Resource Environment, Yichun University, Yichun, 336000, People's Republic of China
| | - Hai-Ming Ma
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, People's Republic of China.
| | - Jun Jiang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, People's Republic of China
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47
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Bonar E, Wojcik I, Jankowska U, Kedracka-Krok S, Bukowski M, Polakowska K, Lis MW, Kosecka-Strojek M, Sabat AJ, Dubin G, Friedrich AW, Miedzobrodzki J, Dubin A, Wladyka B. Identification of Secreted Exoproteome Fingerprints of Highly-Virulent and Non-Virulent Staphylococcus aureus Strains. Front Cell Infect Microbiol 2016; 6:51. [PMID: 27242969 PMCID: PMC4874363 DOI: 10.3389/fcimb.2016.00051] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/19/2016] [Indexed: 12/18/2022] Open
Abstract
Staphylococcus aureus is a commensal inhabitant of skin and mucous membranes in nose vestibule but also an important opportunistic pathogen of humans and livestock. The extracellular proteome as a whole constitutes its major virulence determinant; however, the involvement of particular proteins is still relatively poorly understood. In this study, we compared the extracellular proteomes of poultry-derived S. aureus strains exhibiting a virulent (VIR) and non-virulent (NVIR) phenotype in a chicken embryo experimental infection model with the aim to identify proteomic signatures associated with the particular phenotypes. Despite significant heterogeneity within the analyzed proteomes, we identified alpha-haemolysin and bifunctional autolysin as indicators of virulence, whereas glutamylendopeptidase production was characteristic for non-virulent strains. Staphopain C (StpC) was identified in both the VIR and NVIR proteomes and the latter fact contradicted previous findings suggesting its involvement in virulence. By supplementing NVIR, StpC-negative strains with StpC, and comparing the virulence of parental and supplemented strains, we demonstrated that staphopain C alone does not affect staphylococcal virulence in a chicken embryo model.
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Affiliation(s)
- Emilia Bonar
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Krakow, Poland
| | - Iwona Wojcik
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Krakow, Poland
| | - Urszula Jankowska
- Malopolska Centre of Biotechnology, Jagiellonian University Krakow, Poland
| | - Sylwia Kedracka-Krok
- Malopolska Centre of Biotechnology, Jagiellonian UniversityKrakow, Poland; Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian UniversityKrakow, Poland
| | - Michal Bukowski
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Krakow, Poland
| | - Klaudia Polakowska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Krakow, Poland
| | - Marcin W Lis
- Department of Veterinary and Animal Reproduction and Welfare, Faculty of Animal Welfare, University of Agriculture in Krakow Krakow, Poland
| | - Maja Kosecka-Strojek
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Krakow, Poland
| | - Artur J Sabat
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen Groningen, Netherlands
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian UniversityKrakow, Poland; Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian UniversityKrakow, Poland
| | - Alexander W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen Groningen, Netherlands
| | - Jacek Miedzobrodzki
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Krakow, Poland
| | - Adam Dubin
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Krakow, Poland
| | - Benedykt Wladyka
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Krakow, Poland
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L'Imperio V, Smith A, Chinello C, Pagni F, Magni F. Proteomics and glomerulonephritis: A complementary approach in renal pathology for the identification of chronic kidney disease related markers. Proteomics Clin Appl 2016; 10:371-83. [DOI: 10.1002/prca.201500075] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 10/16/2015] [Accepted: 12/02/2015] [Indexed: 12/25/2022]
Affiliation(s)
| | - Andrew Smith
- Department of Health Sciences; University Milan Bicocca; Monza Italy
| | - Clizia Chinello
- Department of Health Sciences; University Milan Bicocca; Monza Italy
| | - Fabio Pagni
- Department of Pathology; University Milan Bicocca; Monza Italy
| | - Fulvio Magni
- Department of Health Sciences; University Milan Bicocca; Monza Italy
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49
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Candas D, Qin L, Fan M, Li JJ. Experimental Approaches to Study Mitochondrial Localization and Function of a Nuclear Cell Cycle Kinase, Cdk1. J Vis Exp 2016:53417. [PMID: 26967001 DOI: 10.3791/53417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Although mitochondria possess their own transcriptional machinery, merely 1% of mitochondrial proteins are synthesized inside the organelle. The nuclear-encoded proteins are transported into mitochondria guided by their mitochondria targeting sequences (MTS); however, a majority of mitochondrial localized proteins lack an identifiable MTS. Nevertheless, the fact that MTS can instruct proteins to go into the mitochondria provides a valuable tool for studying mitochondrial functions of normally nuclear and/or cytoplasmic proteins. We have recently identified the cell cycle kinase CyclinB1/Cdk1 complex in the mitochondria. To specifically study the mitochondrial functions of this complex, mitochondrial overexpression and knock-down of this complex without interfering with its nuclear or cytoplasmic functions were essential. By tagging CyclinB1/Cdk1 with MTS, we were able to achieve mitochondrial overexpression of this complex to study its mitochondrial targets as well as functions. Via tagging dominant-negative Cdk1 with MTS, inhibition of Cdk1 activity was accomplished particularly in the mitochondria. Potential mitochondrial targets of CyclinB1/Cdk1 complex were identified using a gel-based proteomics approach. Unlike traditional 2D gel analysis, we employed 2-dimensional difference gel electrophoresis (2D-DIGE) technology followed by phosphoprotein staining to fluorescently label differentially phosphorylated proteins in mitochondrial Cdk1 expressing cells. Identification of phosphoprotein spots that were altered in wild type versus dominant negative Cdk1 bearing mitochondria revealed the identity of mitochondrial targets of Cdk1. Finally, to determine the effect of CyclinB1/Cdk1 mitochondrial localization in cell cycle progression, a cell proliferation assay using a synthetic thymidine analogue EdU (5-ethynyl-2'-deoxyuridine) was used to monitor the cells as they go through the cell cycle and replicate their DNA. Altogether, we demonstrated a variety of approaches available to study mitochondrial localization and activity of a cell cycle kinase. These are advanced, yet easy to follow methods that will be beneficial to many cell biology researchers.
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Affiliation(s)
- Demet Candas
- Radiation Oncology, University of California, Davis;
| | - Lili Qin
- Radiation Oncology, University of California, Davis
| | - Ming Fan
- Radiation Oncology, University of California, Davis
| | - Jian-Jian Li
- Radiation Oncology, University of California, Davis
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50
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The evolution of analytical chemistry methods in foodomics. J Chromatogr A 2016; 1428:3-15. [DOI: 10.1016/j.chroma.2015.09.007] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/26/2015] [Accepted: 09/02/2015] [Indexed: 12/18/2022]
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