1
|
Bottoni P, Pontoglio A, Scarà S, Pieroni L, Urbani A, Scatena R. Mitochondrial Respiratory Complexes as Targets of Drugs: The PPAR Agonist Example. Cells 2022; 11:cells11071169. [PMID: 35406733 PMCID: PMC8997591 DOI: 10.3390/cells11071169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/17/2022] [Accepted: 03/24/2022] [Indexed: 12/02/2022] Open
Abstract
Mitochondrial bioenergetics are progressively acquiring significant pathophysiological roles. Specifically, mitochondria in general and Electron Respiratory Chain in particular are gaining importance as unintentional targets of different drugs. The so-called PPAR ligands are a class of drugs which not only link and activate Peroxisome Proliferator-Activated Receptors but also show a myriad of extrareceptorial activities as well. In particular, they were shown to inhibit NADH coenzyme Q reductase. However, the molecular picture of this intriguing bioenergetic derangement has not yet been well defined. Using high resolution respirometry, both in permeabilized and intact HepG2 cells, and a proteomic approach, the mitochondrial bioenergetic damage induced by various PPAR ligands was evaluated. Results show a derangement of mitochondrial oxidative metabolism more complex than one related to a simple perturbation of complex I. In fact, a partial inhibition of mitochondrial NADH oxidation seems to be associated not only with hampered ATP synthesis but also with a significant reduction in respiratory control ratio, spare respiratory capacity, coupling efficiency and, last but not least, serious oxidative stress and structural damage to mitochondria.
Collapse
Affiliation(s)
- Patrizia Bottoni
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Rome, Italy; (A.P.); (S.S.); (A.U.); (R.S.)
- Correspondence:
| | - Alessandro Pontoglio
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Rome, Italy; (A.P.); (S.S.); (A.U.); (R.S.)
| | - Salvatore Scarà
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Rome, Italy; (A.P.); (S.S.); (A.U.); (R.S.)
| | | | - Andrea Urbani
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Rome, Italy; (A.P.); (S.S.); (A.U.); (R.S.)
- Dipartimento di Medicina di Laboratorio, Fondazione Policlinico Gemelli, Largo Agostino Gemelli 8, 00168 Rome, Italy
| | - Roberto Scatena
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Rome, Italy; (A.P.); (S.S.); (A.U.); (R.S.)
- Dipartimento di Medicina di Laboratorio, Madre Giuseppina Vannini Hospital, Via di Acqua Bullicante 4, 00177 Rome, Italy
| |
Collapse
|
2
|
Bazile J, Picard B, Chambon C, Valais A, Bonnet M. Pathways and biomarkers of marbling and carcass fat deposition in bovine revealed by a combination of gel-based and gel-free proteomic analyses. Meat Sci 2019; 156:146-155. [DOI: 10.1016/j.meatsci.2019.05.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/05/2019] [Accepted: 05/16/2019] [Indexed: 01/09/2023]
|
3
|
Kuot A, Ronci M, Mills R, Klebe S, Snibson G, Wiffen S, Loh R, Corbett M, Zhou T, Chataway T, Burdon KP, Craig JE, Urbani A, Sharma S. Reduced expression of apolipoprotein E and immunoglobulin heavy constant gamma 1 proteins in Fuchs endothelial corneal dystrophy. Clin Exp Ophthalmol 2019; 47:1028-1042. [PMID: 31206232 DOI: 10.1111/ceo.13569] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 05/30/2019] [Accepted: 06/05/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND Fuchs endothelial corneal dystrophy (FECD) is a progressive and potentially a sight threatening disease, and a common indication for corneal grafting in the elderly. Aberrant thickening of Descemet's membrane, formation of microscopic excrescences (guttae) and gradual loss of corneal endothelial cells are the hallmarks of the disease. The aim of this study was to identify differentially abundant proteins between FECD-affected and unaffected Descemet's membrane. METHODS Label-free quantitative proteomics using nanoscale ultra-performance liquid chromatography-mass spectrometry (nUPLC-MSE ) was employed on affected and unaffected Descemet's membrane extracts, and interesting findings were further investigated using quantitative reverse transcription-polymerase chain reaction and immunohistochemical techniques. RESULTS Quantitative proteomics revealed significantly lower abundance of apolipoprotein E (APOE) and immunoglobulin heavy constant gamma 1 protein (IGHG1) in affected Descemet's membrane. The difference in the distribution of APOE between affected and unaffected Descemet's membrane and of IGHG1 detected by immunohistochemistry support their down-regulation in the disease. Comparative gene expression analysis showed significantly lower APOE mRNA levels in FECD-affected than unaffected corneal endothelium. IGHG1 gene is expressed at extremely low levels in the corneal endothelium, precluding relative expression analysis. CONCLUSIONS This is the first study to report comparative proteomics of Descemet's membrane tissue, and implicates dysregulation of APOE and IGHG1 proteins in the pathogenesis of Fuchs endothelial corneal dystrophy.
Collapse
Affiliation(s)
- Abraham Kuot
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - Maurizio Ronci
- Department of Medical, Oral and Biotechnological Sciences, University of G. d'Annunzio Chieti Pescara, Pescara, Italy
| | - Richard Mills
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - Sonja Klebe
- Department of Anatomical Pathology, Flinders University, Adelaide, South Australia, Australia
| | - Grant Snibson
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
| | - Steven Wiffen
- The Lions Eye Bank of Western Australia, Lions Eye Institute, Perth, Western Australia, Australia
| | - Raymond Loh
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - Mark Corbett
- Discipline of Paediatrics, School of Medicine and Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Tiger Zhou
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - Tim Chataway
- Department of Human Physiology, Proteomics Laboratory, Flinders University, Adelaide, South Australia, Australia
| | - Kathryn P Burdon
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia.,Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Jamie E Craig
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - Andrea Urbani
- Institute of Biochemistry and Clinical Biochemistry, Università Cattolica del Sacro Cuore, Rome, Italy.,Department of Laboratory Diagnostic and Infectious Diseases, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, Rome, Italy
| | - Shiwani Sharma
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| |
Collapse
|
4
|
Di Venere M, Viglio S, Sassera D, Fumagalli M, Bardoni A, Salvini R, Cagnone M, Iadarola P. Do the complementarities of electrokinetic and chromatographic procedures represent the "Swiss knife" in proteomic investigation? An overview of the literature in the past decade. Electrophoresis 2017; 38:1538-1550. [PMID: 28130906 DOI: 10.1002/elps.201600504] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/11/2017] [Accepted: 01/11/2017] [Indexed: 12/21/2022]
Abstract
This report reviews the literature of the past decade dealing with the combination of electrokinetic and chromatographic strategies in the proteomic field. Aim of this article is to highlight how the application of complementary techniques may contribute to substantially improve protein identification. Several studies here considered demonstrate that exploring the combination of these approaches can be a strategy to enrich the extent of proteomic information achieved from a sample. The coupling of "top-down" and "bottom-up" proteomics may result in the generation of a hybrid analytical tool, very efficient not only for large-scale profiling of complex proteomes but also for studying specific subproteomes. The range of applications described, while evidencing a continuous boost in the imagination of researchers for developing new combinations of methods for protein separation, also underlines the adaptability of these techniques to a wide variety of samples. This report points out the general usefulness of combining different procedures for proteomic analysis, an approach that allows researchers to go deeper in the proteome of samples under investigation.
Collapse
Affiliation(s)
- Monica Di Venere
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Simona Viglio
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Davide Sassera
- Department of Biology and Biotechnologies "L. Spallanzani,", Biochemistry Unit, University of Pavia, Italy
| | - Marco Fumagalli
- Department of Biology and Biotechnologies "L. Spallanzani,", Biochemistry Unit, University of Pavia, Italy
| | - Anna Bardoni
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Roberta Salvini
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Maddalena Cagnone
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Paolo Iadarola
- Department of Biology and Biotechnologies "L. Spallanzani,", Biochemistry Unit, University of Pavia, Italy
| |
Collapse
|
5
|
Izquierdo I, García Á. Platelet proteomics applied to the search for novel antiplatelet therapeutic targets. Expert Rev Proteomics 2016; 13:993-1006. [DOI: 10.1080/14789450.2016.1246188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
6
|
Maloney JP, Narasimhan J, Biller J. Decreased TGF-β1 and VEGF Release in Cystic Fibrosis Platelets: Further Evidence for Platelet Defects in Cystic Fibrosis. Lung 2016; 194:791-8. [PMID: 27423781 DOI: 10.1007/s00408-016-9925-9] [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: 03/30/2016] [Accepted: 07/11/2016] [Indexed: 12/11/2022]
Abstract
PURPOSE Cystic fibrosis (CF) patients suffer from chronic lung inflammation. This inflammation may activate platelets. There are limited data on the role of platelet-secreted cytokines in CF. Platelet cytokines with inflammatory effects include vascular endothelial growth factor (VEGF) and transforming growth factor-β1 (TGF-β1). As levels of these cytokines are tenfold greater in serum than plasma due to platelet release, serum levels may be one index of platelet content, but a more specific index is release during the aggregation of isolated platelets. We postulated that altered release of these platelet cytokines occurs in CF. METHODS We obtained sera and plasma from CF outpatients (n = 21) and from healthy controls (n = 20), measured VEGF and TGF-β1, assessed for correlations with platelet number, analyzed cytokine release during platelet aggregation to collagen, and analyzed differences in maximal platelet aggregation. RESULTS Platelet number and maximal aggregation levels were higher in CF. Plasma and serum levels of TGF-β1 and VEGF were higher in CF, but these levels were similar after adjusting for platelet number (serum cytokines correlated with platelet count). The release of VEGF and TGF-β1 during aggregation was decreased in CF platelets (by 52 and 29 %, respectively). CONCLUSION Platelet release is not a source of the elevated blood proinflammatory cytokines TGF-β1 and VEGF in CF, as platelets from CF patients actually release less of these cytokines. These data provide further evidence for platelet defects in CF.
Collapse
Affiliation(s)
- James P Maloney
- Divisions of Pulmonary and Critical Care Medicine, University of Colorado, Denver, 12700 East 19th Avenue, C-272, Aurora, Denver, CO, 80045, USA.
| | | | - Julie Biller
- The Medical College of Wisconsin, Milwaukee, WI, USA
| |
Collapse
|
7
|
García Á. Platelet clinical proteomics: Facts, challenges, and future perspectives. Proteomics Clin Appl 2016; 10:767-73. [PMID: 26948058 DOI: 10.1002/prca.201500125] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 02/17/2016] [Accepted: 02/29/2016] [Indexed: 11/08/2022]
Abstract
In recent years, proteomics has been applied to platelet clinical research. Platelets are small enucleated cells that play a fundamental role in hemostasis. In a pathological context, unwanted platelet activation is related to various diseases, primarily thrombosis, but also cancer metastasis, inflammation, immunity, and neurodegenerative diseases. The absence of a nucleus is one of the reasons why proteomics can be considered an ideal analytical tool for platelet research. Indeed, platelet proteomics has allowed the identification of many novel signaling proteins and receptors, several of which are being pursued as potential therapeutic targets. Encouraged by this success, several research groups have recently initiated clinical proteomics studies covering diseases where platelets are involved in some way, such as coronary artery disease, storage pool diseases, uremia, cystic fibrosis, and Alzheimer disease. The goal was to identify platelet biomarkers and drug targets that can help to improve the treatment/diagnosis of the disease and provide further mechanistic evidences of the role platelets play in the pathology. The present article will comment on the recent progress of clinical proteomics in the context of platelet research, challenges, and perspectives for the future ahead.
Collapse
Affiliation(s)
- Ángel García
- Platelet Proteomics Group, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, and Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| |
Collapse
|
8
|
Vacca V, Marinelli S, Pieroni L, Urbani A, Luvisetto S, Pavone F. 17beta-estradiol counteracts neuropathic pain: a behavioural, immunohistochemical, and proteomic investigation on sex-related differences in mice. Sci Rep 2016; 6:18980. [PMID: 26742647 PMCID: PMC4705539 DOI: 10.1038/srep18980] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 09/02/2015] [Indexed: 01/31/2023] Open
Abstract
Sex differences play a role in pain sensitivity, efficacy of analgesic drugs and prevalence of neuropathic pain, even if the underlying mechanisms are far from being understood. We demonstrate that male and female mice react differently to structural and functional changes induced by sciatic nerve ligature, used as model of neuropathic pain. Male mice show a gradual decrease of allodynia and a complete recovery while, in females, allodynia and gliosis are still present four months after neuropathy induction. Administration of 17β-estradiol is able to significantly attenuate this difference, reducing allodynia and inducing a complete recovery also in female mice. Parallel to pain attenuation, 17β-estradiol treated-mice show a functional improvement of the injured limb, a faster regenerative process of the peripheral nerve and a decreased neuropathy-induced gliosis. These results indicate beneficial effects of 17β-estradiol on neuropathic pain and neuronal regeneration and focuses on the importance of considering gonadal hormones also in clinical studies.
Collapse
Affiliation(s)
- Valentina Vacca
- CNR-National Research Council, Institute of Cell Biology and Neurobiology, 00143 Roma, Italy.,IRCCS Fondazione Santa Lucia, 00143 Roma, Italy
| | - Sara Marinelli
- CNR-National Research Council, Institute of Cell Biology and Neurobiology, 00143 Roma, Italy.,IRCCS Fondazione Santa Lucia, 00143 Roma, Italy
| | - Luisa Pieroni
- IRCCS Fondazione Santa Lucia, 00143 Roma, Italy.,Department of Experimental Medicine and Surgery, Division of Biochemistry, University of "Tor Vergata", 00133 Roma, Italy
| | - Andrea Urbani
- IRCCS Fondazione Santa Lucia, 00143 Roma, Italy.,Department of Experimental Medicine and Surgery, Division of Biochemistry, University of "Tor Vergata", 00133 Roma, Italy
| | - Siro Luvisetto
- CNR-National Research Council, Institute of Cell Biology and Neurobiology, 00143 Roma, Italy.,IRCCS Fondazione Santa Lucia, 00143 Roma, Italy
| | - Flaminia Pavone
- CNR-National Research Council, Institute of Cell Biology and Neurobiology, 00143 Roma, Italy.,IRCCS Fondazione Santa Lucia, 00143 Roma, Italy
| |
Collapse
|
9
|
Foglio E, Puddighinu G, Fasanaro P, D'Arcangelo D, Perrone GA, Mocini D, Campanella C, Coppola L, Logozzi M, Azzarito T, Marzoli F, Fais S, Pieroni L, Marzano V, Germani A, Capogrossi MC, Russo MA, Limana F. Exosomal clusterin, identified in the pericardial fluid, improves myocardial performance following MI through epicardial activation, enhanced arteriogenesis and reduced apoptosis. Int J Cardiol 2015; 197:333-47. [PMID: 26159041 DOI: 10.1016/j.ijcard.2015.06.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 05/13/2015] [Accepted: 06/12/2015] [Indexed: 12/23/2022]
Abstract
BACKGROUND We recently demonstrated that epicardial progenitor cells participate in the regenerative response to myocardial infarction (MI) and factors released in the pericardial fluid (PF) may play a key role in this process. Exosomes are secreted nanovesicles of endocytic origin, identified in most body fluids, which may contain molecules able to modulate a variety of cell functions. Here, we investigated whether exosomes are present in the PF and their potential role in cardiac repair. METHODS AND RESULTS Early gene expression studies in 3day-infarcted mouse hearts showed that PF induces epithelial-to-mesenchymal transition (EMT) in epicardial cells. Exosomes were identified in PFs from non-infarcted patients (PFC) and patients with acute MI (PFMI). A shotgun proteomics analysis identified clusterin in exosomes isolated from PFMI but not from PFC. Notably, clusterin has a protective effect on cardiomyocytes after acute MI in vivo and is an important mediator of TGFβ-induced. Clusterin addition to the pericardial sac determined an increase in epicardial cells expressing the EMT marker α-SMA and, interestingly, an increase in the number of epicardial cells ckit(+)/α-SMA(+), 7days following MI. Importantly, clusterin treatment enhanced arteriolar length density and lowered apoptotic rates in the peri-infarct area. Hemodynamic studies demonstrated an improvement in cardiac function in clusterin-treated compared to untreated infarcted hearts. CONCLUSIONS Exosomes are present and detectable in the PFs. Clusterin was identified in PFMI-exosomes and might account for an improvement in myocardial performance following MI through a framework including EMT-mediated epicardial activation, arteriogenesis and reduced cardiomyocyte apoptosis.
Collapse
Affiliation(s)
- Eleonora Foglio
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Giovanni Puddighinu
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Pasquale Fasanaro
- Epigenetics & Regenerative Pharmacology, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Daniela D'Arcangelo
- Laboratorio di Patologia Vascolare, Istituto Dermopatico dell'Immacolata, IRCCS, Rome, Italy
| | | | | | | | | | - Mariantonia Logozzi
- Department of Therapeutic Research and Medicines Evaluation, National Institute of Health, Italy
| | - Tommaso Azzarito
- Department of Therapeutic Research and Medicines Evaluation, National Institute of Health, Italy
| | - Francesca Marzoli
- Department of Therapeutic Research and Medicines Evaluation, National Institute of Health, Italy
| | - Stefano Fais
- Department of Therapeutic Research and Medicines Evaluation, National Institute of Health, Italy
| | - Luisa Pieroni
- Dipartimento di Medicina Sperimentale e Chirurgia, Facoltà di Medicina e Chirurgia, Università' di Roma "Tor Vergata", Italy
| | - Valeria Marzano
- Institute of Chemistry of Molecular Recognition, Italian National Research Council (CNR), Rome, Italy
| | - Antonia Germani
- Laboratorio di Patologia Vascolare, Istituto Dermopatico dell'Immacolata, IRCCS, Rome, Italy
| | - Maurizio C Capogrossi
- Laboratorio di Patologia Vascolare, Istituto Dermopatico dell'Immacolata, IRCCS, Rome, Italy
| | - Matteo A Russo
- Laboratorio di Patologia Cellulare e Molecolare, San Raffaele Pisana, Istituto di Ricovero e Cura a Carattere Scientifico - IRCCS, Rome, Italy
| | - Federica Limana
- Laboratorio di Patologia Cellulare e Molecolare, San Raffaele Pisana, Istituto di Ricovero e Cura a Carattere Scientifico - IRCCS, Rome, Italy.
| |
Collapse
|
10
|
Mancini F, Pieroni L, Monteleone V, Lucà R, Fici L, Luca E, Urbani A, Xiong S, Soddu S, Masetti R, Lozano G, Pontecorvi A, Moretti F. MDM4/HIPK2/p53 cytoplasmic assembly uncovers coordinated repression of molecules with anti-apoptotic activity during early DNA damage response. Oncogene 2015; 35:228-40. [PMID: 25961923 PMCID: PMC4717155 DOI: 10.1038/onc.2015.76] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 02/02/2015] [Accepted: 02/18/2015] [Indexed: 12/14/2022]
Abstract
The p53 inhibitor, MDM4 (MDMX) is a cytoplasmic protein with p53-activating function under DNA damage conditions. Particularly, MDM4 promotes phosphorylation of p53 at Ser46, a modification that precedes different p53 activities. We investigated the mechanism by which MDM4 promotes this p53 modification and its consequences in untransformed mammary epithelial cells and tissues. In response to severe DNA damage, MDM4 stimulates p53Ser46P by binding and stabilizing serine–threonine kinase HIPK2. Under these conditions, the p53-inhibitory complex, MDM4/MDM2, dissociates and this allows MDM4 to promote p53/HIPK2 functional interaction. Comparative proteomic analysis of DNA damage-treated cells versus -untreated cells evidenced a diffuse downregulation of proteins with anti-apoptotic activity, some of which were targets of p53Ser46P/HIPK2 repressive activity. Importantly, MDM4 depletion abolishes the downregulation of these proteins indicating the requirement of MDM4 to promote p53-mediated transcriptional repression. Consistently, MDM4-mediated HIPK2/p53 activation precedes HIPK2/p53 nuclear translocation and activity. Noteworthy, repression of these proteins was evident also in mammary glands of mice subjected to γ-irradiation and was significantly enhanced in transgenic mice overexpressing MDM4. This study evidences the flexibility of MDM2/MDM4 heterodimer, which allows the development of a positive activity of cytoplasmic MDM4 towards p53-mediated transcriptional function. Noteworthy, this activity uncovers coordinated repression of molecules with shared anti-apoptotic function which precedes active cell apoptosis and that are frequently overexpressed and/or markers of tumour phenotype in human cancer.
Collapse
Affiliation(s)
- F Mancini
- Institute of Cell Biology and Neurobiology, National Research Council of Italy (CNR), Roma, Italy.,Department of Endocrinology and Metabolism, Catholic University of Roma, Roma, Italy
| | - L Pieroni
- Proteomic and Metabolomic Laboratory, Fondazione Santa Lucia, Roma, Italy.,Department of Experimental Medicine and Surgery, University of Roma 'Tor Vergata', Roma, Italy
| | - V Monteleone
- Institute of Cell Biology and Neurobiology, National Research Council of Italy (CNR), Roma, Italy
| | - R Lucà
- Institute of Cell Biology and Neurobiology, National Research Council of Italy (CNR), Roma, Italy
| | - L Fici
- Institute of Cell Biology and Neurobiology, National Research Council of Italy (CNR), Roma, Italy.,Department of Obstetrics and Gynaecology, Catholic University of Roma, Roma, Italy
| | - E Luca
- Institute of Cell Biology and Neurobiology, National Research Council of Italy (CNR), Roma, Italy.,Department of Endocrinology and Metabolism, Catholic University of Roma, Roma, Italy
| | - A Urbani
- Proteomic and Metabolomic Laboratory, Fondazione Santa Lucia, Roma, Italy.,Department of Experimental Medicine and Surgery, University of Roma 'Tor Vergata', Roma, Italy
| | - S Xiong
- Department of Genetics, M.D. Anderson Cancer Center, Houston, TX, USA
| | - S Soddu
- Regina Elena National Cancer Institute, Roma, Italy
| | - R Masetti
- Department of Obstetrics and Gynaecology, Catholic University of Roma, Roma, Italy
| | - G Lozano
- Department of Genetics, M.D. Anderson Cancer Center, Houston, TX, USA
| | - A Pontecorvi
- Department of Endocrinology and Metabolism, Catholic University of Roma, Roma, Italy
| | - F Moretti
- Institute of Cell Biology and Neurobiology, National Research Council of Italy (CNR), Roma, Italy
| |
Collapse
|
11
|
Pieroni L, Levi Mortera S, Greco V, Sirolli V, Ronci M, Felaco P, Fucci G, De Fulviis S, Massoud R, Condò S, Capria A, Di Daniele N, Bernardini S, Urbani A, Bonomini M. Biocompatibility assessment of haemodialysis membrane materials by proteomic investigations. MOLECULAR BIOSYSTEMS 2015; 11:1633-43. [DOI: 10.1039/c5mb00058k] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We examine and compare the protein adsorption capacity and coagulation profiles of different haemodialysis membrane biomaterials.
Collapse
|
12
|
Ronci M, Catanzaro G, Pieroni L, Po A, Besharat ZM, Greco V, Levi Mortera S, Screpanti I, Ferretti E, Urbani A. Proteomic analysis of human sonic hedgehog (SHH) medulloblastoma stem-like cells. MOLECULAR BIOSYSTEMS 2015; 11:1603-11. [DOI: 10.1039/c5mb00034c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
First proteomic characterization of sonic hedgehog human medulloblastoma stem-like cells.
Collapse
Affiliation(s)
- Maurizio Ronci
- Department of Medical
- Oral and Biotechnological Sciences
- University G. d'Annunzio of Chieti-Pescara
- Chieti
- Italy
| | - Giuseppina Catanzaro
- Departments of Molecular Medicine and Experimental Medicine University of Sapienza
- Rome
- Italy
| | - Luisa Pieroni
- Santa Lucia IRCCS Foundation
- Rome
- Italy
- Department of Experimental Medicine and Surgery
- University of Rome “Tor Vergata”
| | - Agnese Po
- Departments of Molecular Medicine and Experimental Medicine University of Sapienza
- Rome
- Italy
| | - Zein Mersini Besharat
- Departments of Molecular Medicine and Experimental Medicine University of Sapienza
- Rome
- Italy
| | - Viviana Greco
- Santa Lucia IRCCS Foundation
- Rome
- Italy
- Department of Experimental Medicine and Surgery
- University of Rome “Tor Vergata”
| | - Stefano Levi Mortera
- Santa Lucia IRCCS Foundation
- Rome
- Italy
- Department of Experimental Medicine and Surgery
- University of Rome “Tor Vergata”
| | - Isabella Screpanti
- Departments of Molecular Medicine and Experimental Medicine University of Sapienza
- Rome
- Italy
- Center for Life NanoScience@Sapienza
- Istituto Italiano di Tecnologia
| | - Elisabetta Ferretti
- Departments of Molecular Medicine and Experimental Medicine University of Sapienza
- Rome
- Italy
| | - Andrea Urbani
- Santa Lucia IRCCS Foundation
- Rome
- Italy
- Department of Experimental Medicine and Surgery
- University of Rome “Tor Vergata”
| |
Collapse
|
13
|
Burkhart JM, Gambaryan S, Watson SP, Jurk K, Walter U, Sickmann A, Heemskerk JWM, Zahedi RP. What can proteomics tell us about platelets? Circ Res 2014; 114:1204-19. [PMID: 24677239 DOI: 10.1161/circresaha.114.301598] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
More than 130 years ago, it was recognized that platelets are key mediators of hemostasis. Nowadays, it is established that platelets participate in additional physiological processes and contribute to the genesis and progression of cardiovascular diseases. Recent data indicate that the platelet proteome, defined as the complete set of expressed proteins, comprises >5000 proteins and is highly similar between different healthy individuals. Owing to their anucleate nature, platelets have limited protein synthesis. By implication, in patients experiencing platelet disorders, platelet (dys)function is almost completely attributable to alterations in protein expression and dynamic differences in post-translational modifications. Modern platelet proteomics approaches can reveal (1) quantitative changes in the abundance of thousands of proteins, (2) post-translational modifications, (3) protein-protein interactions, and (4) protein localization, while requiring only small blood donations in the range of a few milliliters. Consequently, platelet proteomics will represent an invaluable tool for characterizing the fundamental processes that affect platelet homeostasis and thus determine the roles of platelets in health and disease. In this article we provide a critical overview on the achievements, the current possibilities, and the future perspectives of platelet proteomics to study patients experiencing cardiovascular, inflammatory, and bleeding disorders.
Collapse
Affiliation(s)
- Julia M Burkhart
- From the Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany (J.M.B., A.S., R.P.Z); Institut für Klinische Biochemie und Pathobiochemie, Universitätsklinikum Würzburg, Würzburg, Germany (S.G.); Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, St. Petersburg, Russia (S.G.); Centre for Cardiovascular Sciences, Institute for Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom (S.P.W.); Center for Thrombosis and Hemostasis, Universitätsklinikum der Johannes Gutenberg-Universität Mainz, Mainz, Germany (K.J., U.W.); Medizinisches Proteom Center, Ruhr Universität Bochum, Bochum, Germany (A.S.); Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom (A.S.); and Department of Biochemistry, CARIM, Maastricht University, Maastricht, The Netherlands (J.W.M.H.)
| | | | | | | | | | | | | | | |
Collapse
|
14
|
UPLC–MSE application in disease biomarker discovery: The discoveries in proteomics to metabolomics. Chem Biol Interact 2014; 215:7-16. [DOI: 10.1016/j.cbi.2014.02.014] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 02/14/2014] [Accepted: 02/28/2014] [Indexed: 01/05/2023]
|
15
|
Alberio T, Bondi H, Colombo F, Alloggio I, Pieroni L, Urbani A, Fasano M. Mitochondrial proteomics investigation of a cellular model of impaired dopamine homeostasis, an early step in Parkinson's disease pathogenesis. MOLECULAR BIOSYSTEMS 2014; 10:1332-44. [PMID: 24675778 DOI: 10.1039/c3mb70611g] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Impaired dopamine homeostasis is an early event in the pathogenesis of Parkinson's disease. Generation of intracellular reactive oxygen species consequent to dopamine oxidation leads to mitochondrial dysfunction and eventually cell death. Alterations in the mitochondrial proteome due to dopamine exposure were investigated in the SH-SY5Y human neuroblastoma cell line. The combination of two orthogonal proteomic approaches, two-dimensional electrophoresis and shotgun proteomics (proteomeXchange dataset PXD000838), was used to highlight the specific pathways perturbed by the increase of intracellular dopamine, in comparison with those perturbed by a specific mitochondrial toxin (4-methylphenylpyridinium, MPP(+)), a neurotoxin causing Parkinsonism-like symptoms in animal models. Proteins altered by MPP(+) did not completely overlap with those affected by dopamine treatment. In particular, the MPP(+) target complex I component NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 was not affected by dopamine together with 26 other proteins. The comparison of proteomics approaches highlighted the fragmentation of some mitochondrial proteins, suggesting an alteration of the mitochondrial protease activity. Pathway and disease association analysis of the proteins affected by dopamine revealed the overrepresentation of the Parkinson's disease and the parkin-ubiquitin proteasomal system pathways and of gene ontologies associated with generation of precursor metabolites and energy, response to topologically incorrect proteins and programmed cell death. These alterations may be globally interpreted in part as the result of a direct effect of dopamine on mitochondria (e.g. alteration of the mitochondrial protease activity) and in part as the effect on mitochondria of a general activation of cellular processes (e.g. regulation of programmed cell death).
Collapse
Affiliation(s)
- Tiziana Alberio
- Biomedical Research Division, Department of Theoretical and Applied Sciences, University of Insubria, Busto Arsizio, Italy.
| | | | | | | | | | | | | |
Collapse
|
16
|
Marinelli S, Nazio F, Tinari A, Ciarlo L, D'Amelio M, Pieroni L, Vacca V, Urbani A, Cecconi F, Malorni W, Pavone F. Schwann cell autophagy counteracts the onset and chronification of neuropathic pain. Pain 2014; 155:93-107. [DOI: 10.1016/j.pain.2013.09.013] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 09/10/2013] [Accepted: 09/10/2013] [Indexed: 11/24/2022]
|
17
|
Analysis of subcellular metabolite distributions within Arabidopsis thaliana leaf tissue: a primer for subcellular metabolomics. Methods Mol Biol 2014; 1062:575-96. [PMID: 24057387 DOI: 10.1007/978-1-62703-580-4_30] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Every biological organism relies for its proper function on interactions between a multitude of molecular entities like RNA, proteins, and metabolites. The comprehensive measurement and the analysis of all these entities would therefore provide the basis for our functional and mechanistic understanding of most biological processes. Next to their amount and identity, it is most crucial to also gain information about the subcellular distribution and the flux of the measured compounds between the cellular compartments. That is, we want to understand not only the individual functions of cellular components but also their functional implications within the whole organism. While the analysis of macromolecules like DNA, RNA, and proteins is quite established and robust, analytical techniques for small metabolites, which are prone to diffusion and degradation processes, provide a host of unsolved challenges. The major limitations here are the metabolite conversion and relocation processes. In this protocol we describe a methodological workflow which includes a nonaqueous fractionation method, a fractionated two-phase liquid/liquid extraction protocol, and a software package, which together allow extracting and analyzing starch, proteins, and especially polar and lipophilic metabolites from a single sample towards the estimation of their subcellular distributions.
Collapse
|
18
|
Vacca V, Marinelli S, Pieroni L, Urbani A, Luvisetto S, Pavone F. Higher pain perception and lack of recovery from neuropathic pain in females: a behavioural, immunohistochemical, and proteomic investigation on sex-related differences in mice. Pain 2013; 155:388-402. [PMID: 24231652 DOI: 10.1016/j.pain.2013.10.027] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 10/30/2013] [Accepted: 10/30/2013] [Indexed: 01/23/2023]
Abstract
In experimental and clinical pain studies, the sex of subjects was rarely taken into account, even if nociceptive inputs appear to be processed and modulated by partially distinct neural mechanisms in each sex. In this study we analysed, in male and female mice, behavioural and neuronal responses in developing, maintaining, and recovering from neuropathic pain. Experiments were carried out in adult CD1 mice by using Chronic Constriction Injury (CCI) as neuropathic pain model. We investigated the temporal trend of mechanical nociceptive threshold together with functional recovery of the injured paw, and the immunofluorescence staining of proteins associated with nerve injury and repair and with spinal gliosis, 7 and 121days after CCI. A proteomic analysis on proteins extracted from sciatic nerves was also performed. Male mice showed a gradual decrease of CCI-induced allodynia, the complete recovery occurring 81days after the sciatic nerve ligation. On the contrary, in female mice, allodynia was still present 121days after CCI. Sex-dependent differences also resulted from immunofluorescence experiments: in sciatic nerve, the expression of P0 and Neu200 is greater in neuropathic males than in neuropathic females, suggesting faster nerve regeneration. Proteomic analysis confirmed sex-related differences of proteins associated with nerve regenerative processes. In addition, the reactive gliosis induced by CCI at day 7, as revealed by colocalization of glial fibrillary acidic protein (astrocytes) and CD11b (microglia) with phosphorylated p38, disappeared 121 days after CCI in male but not in female mice. These results may have important therapeutic implications for the treatment of neuropathic pain.
Collapse
Affiliation(s)
- Valentina Vacca
- CNR - National Research Council, Cell Biology and Neurobiology Institute, Roma, Italy IRCCS Santa Lucia Foundation, Roma, Italy Department of Experimental Medicine and Surgery, Division of Biochemistry, University of "Tor Vergata", Roma, Italy
| | | | | | | | | | | |
Collapse
|
19
|
Wickramasekara SI, Zandkarimi F, Morré J, Kirkwood J, Legette L, Jiang Y, Gombart AF, Stevens JF, Maier CS. Electrospray Quadrupole Travelling Wave Ion Mobility Time-of-Flight Mass Spectrometry for the Detection of Plasma Metabolome Changes Caused by Xanthohumol in Obese Zucker (fa/fa) Rats. Metabolites 2013; 3:701-17. [PMID: 24958146 PMCID: PMC3901285 DOI: 10.3390/metabo3030701] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 08/01/2013] [Accepted: 08/07/2013] [Indexed: 12/12/2022] Open
Abstract
This study reports on the use of traveling wave ion mobility quadrupole time-of-flight (ToF) mass spectrometry for plasma metabolomics. Plasma metabolite profiles of obese Zucker fa/fa rats were obtained after the administration of different oral doses of Xanthohumol; a hop-derived dietary supplement. Liquid chromatography coupled data independent tandem mass spectrometry (LC-MSE) and LC-ion mobility spectrometry (IMS)-MSE acquisitions were conducted in both positive and negative modes using a Synapt G2 High Definition Mass Spectrometry (HDMS) instrument. This method provides identification of metabolite classes in rat plasma using parallel alternating low energy and high energy collision spectral acquisition modes. Data sets were analyzed using pattern recognition methods. Statistically significant (p < 0.05 and fold change (FC) threshold > 1.5) features were selected to identify the up-/down-regulated metabolite classes. Ion mobility data visualized using drift scope software provided a graphical read-out of differences in metabolite classes.
Collapse
Affiliation(s)
| | | | - Jeff Morré
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA.
| | - Jay Kirkwood
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331, USA.
| | - LeeCole Legette
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331, USA.
| | - Yuan Jiang
- Department of Statistics, Oregon State University, Corvallis, OR 97331, USA.
| | - Adrian F Gombart
- Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, USA.
| | - Jan F Stevens
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331, USA.
| | - Claudia S Maier
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA.
| |
Collapse
|
20
|
Ronci M, Sharma S, Martin S, Craig JE, Voelcker NH. MALDI MS imaging analysis of apolipoprotein E and lysyl oxidase-like 1 in human lens capsules affected by pseudoexfoliation syndrome. J Proteomics 2013; 82:27-34. [PMID: 23411028 DOI: 10.1016/j.jprot.2013.01.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Revised: 01/09/2013] [Accepted: 01/11/2013] [Indexed: 01/06/2023]
Abstract
UNLABELLED Pseudoexfoliation (PEX) syndrome is an age-related systemic disease of the extracellular matrix, characterized by the presence of amyloid-like fibrillar deposits on the anterior lens capsule. The pathological deposits (PEX material) can obstruct aqueous outflow leading to increased intraocular pressure that in turn can result in glaucoma. PEX syndrome is the most common risk factor for glaucoma. In our previous work, we reported a protocol for the analysis of human lens capsules by MALDI MS imaging. Here, we extend our previous work applying the developed protocol to the analysis of human lens capsules affected by PEX syndrome. We focus our investigation on known components of the PEX material, namely lysyl oxidase-like 1 (LOXL1) and apolipoprotein E (APOE). Our results show that LOXL1 is more abundant in the deposits in the iris region and, alternatively APOE is concentrated in the PEX material accumulated in the pupillary area of the anterior lens capsule. Furthermore, we identify potentially relevant post-translational modifications which may have an important role in promoting the cross-linking processes in PEX syndrome and stabilize aggregate structures within the proteinaceous PEX material. BIOLOGICAL SIGNIFICANCE This paper is about the identification and localization of apolipoprotein E and lysyl oxidase-like 1 in human lens capsules affected by PEX syndrome by MALDI MS imaging. With this study we expand the clinical application of MALDI MSI toward the use of non-sectioned tissue samples analyzed after in situ enzymatic digestion and advance the knowledge regarding a common pathology like PEX syndrome.
Collapse
Affiliation(s)
- Maurizio Ronci
- Mawson Institute, University of South Australia, Mawson Lakes SA 5095, Australia.
| | | | | | | | | |
Collapse
|
21
|
Zufferey A, Ibberson M, Reny JL, Xenarios I, Sanchez JC, Fontana P. Unraveling modulators of platelet reactivity in cardiovascular patients using omics strategies: Towards a network biology paradigm. TRANSLATIONAL PROTEOMICS 2013. [DOI: 10.1016/j.trprot.2013.04.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
|
22
|
|
23
|
Ciavardelli D, D'Orazio M, Pieroni L, Consalvo A, Rossi C, Sacchetta P, Di Ilio C, Battistoni A, Urbani A. Proteomic and ionomic profiling reveals significant alterations of protein expression and calcium homeostasis in cystic fibrosis cells. MOLECULAR BIOSYSTEMS 2013; 9:1117-26. [DOI: 10.1039/c3mb25594h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
24
|
Parguiña AF, Rosa I, García Á. Proteomics applied to the study of platelet-related diseases: Aiding the discovery of novel platelet biomarkers and drug targets. J Proteomics 2012; 76 Spec No.:275-86. [DOI: 10.1016/j.jprot.2012.04.043] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 04/24/2012] [Accepted: 04/26/2012] [Indexed: 01/04/2023]
|
25
|
Proteomic investigations on the effect of different membrane materials on blood protein adsorption during haemodialysis. BLOOD TRANSFUSION = TRASFUSIONE DEL SANGUE 2012; 10 Suppl 2:s101-12. [PMID: 22890260 DOI: 10.2450/2012.014s] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
BACKGROUND During haemodialysis procedure, the contact of blood with the membrane material contained in the hemodialyser results in protein deposition and adsorption, and surface-adsorbed proteins may trigger a variety of biological pathways with potential pathophysiologic consequences. The present work was undertaken to examine for protein adsorption capacity of two membranes used for clinical haemodialysis, namely cellulose triacetate (a derivatized cellulosic membrane) and the synthetic polymer polysulfone-based helixone. MATERIALS AND METHODS We performed a prospective cross-over study in chronic haemodialysis patients, routinely treated with a cellulose triacetate dialyser (n=3) or with a helixone dialyser (n=3). Dialysers from each patient were obtained after dialysis session, and flushed with a litre of saline to remove residual blood. Adsorbed proteins were then eluted by a strong chaotropic buffer. Patients were next switched to the other membrane dialyser for four weeks, at the end of this period protein adsorption being evaluated again. After silver staining, expression profile protein of the two groups was analyzed by 2-DE gels, analyzed and identified by Peptide Mass-finger printing and MALDI-TOF-MS/MS sequency. Moreover nanoLC-MS/MS shotgun profiling was pursued using a semi-quantitative label free approach by emPAI data analysis. RESULTS A total of 54 differentially expressed proteins were identified: 22 proteins more concentrated in helixone membrane (predominantly low abundant plasma proteins) and 32 in cellulose triacetate (most represented by high abundant plasma proteins). The difference proved to be related to membrane material and not to patient's characteristics. DISCUSSION Proteomic techniques represent a useful approach for the investigation of proteins surface-adsorbed onto a haemodialysis membrane, and can also be applied for critical assessment to compare efficiencies of different dialyser membrane materials in the adsorption of plasma proteins.
Collapse
|
26
|
Eiserich JP, Yang J, Morrissey BM, Hammock BD, Cross CE. Omics approaches in cystic fibrosis research: a focus on oxylipin profiling in airway secretions. Ann N Y Acad Sci 2012; 1259:1-9. [PMID: 22758630 DOI: 10.1111/j.1749-6632.2012.06580.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cystic fibrosis (CF) is associated with abnormal lipid metabolism, intense respiratory tract (RT) infection, and inflammation, eventually resulting in lung tissue destruction and respiratory failure. The CF RT inflammatory milieu, as reflected by airway secretions, includes a complex array of inflammatory mediators, bacterial products, and host secretions. It is dominated by neutrophils and their proteolytic and oxidative products and includes a wide spectrum of bioactive lipids produced by both host and presumably microbial metabolic pathways. The fairly recent advent of "omics" technologies has greatly increased capabilities of further interrogating this easily obtainable RT compartment that represents the apical culture media of the underlying RT epithelial cells. This paper discusses issues related to the study of CF omics with a focus on the profiling of CF RT oxylipins. Challenges in their identification/quantitation in RT fluids, their pathways of origin, and their potential utility for understanding CF RT inflammatory and oxidative processes are highlighted. Finally, the utility of oxylipin metabolic profiling in directing optimal therapeutic approaches and determining the efficacy of various interventions is discussed.
Collapse
Affiliation(s)
- Jason P Eiserich
- Department of Internal Medicine, University of California, Davis, California, USA
| | | | | | | | | |
Collapse
|
27
|
Zufferey A, Fontana P, Reny JL, Nolli S, Sanchez JC. Platelet proteomics. MASS SPECTROMETRY REVIEWS 2012; 31:331-351. [PMID: 22009795 DOI: 10.1002/mas.20345] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 06/10/2011] [Accepted: 06/10/2011] [Indexed: 05/31/2023]
Abstract
Platelets are small cell fragments, produced by megakaryocytes, in the bone marrow. They play an important role in hemostasis and diverse thrombotic disorders. They are therefore primary targets of antithrombotic therapies. They are implicated in several pathophysiological pathways, such as inflammation or wound repair. In blood circulation, platelets are activated by several pathways including subendothelial matrix and thrombin, triggering the formation of the platelet plug. Studying their proteome is a powerful approach to understand their biology and function. However, particular attention must be paid to different experimental parameters, such as platelet quality and purity. Several technologies are involved during the platelet proteome processing, yielding information on protein identification, characterization, localization, and quantification. Recent technical improvements in proteomics combined with inter-disciplinary strategies, such as metabolomic, transcriptomics, and bioinformatics, will help to understand platelets biological mechanisms. Therefore, a comprehensive analysis of the platelet proteome under different environmental conditions may contribute to elucidate complex processes relevant to platelet function regarding bleeding disorders or platelet hyperreactivity and identify new targets for antiplatelet therapy.
Collapse
Affiliation(s)
- Anne Zufferey
- Division of Angiology and Haemostasis, Department of Internal Medicine, Faculty of Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | | | | | | | | |
Collapse
|
28
|
Banci L, Bertini I, Ciofi-Baffoni S, D'Alessandro A, Jaiswal D, Marzano V, Neri S, Ronci M, Urbani A. Copper exposure effects on yeast mitochondrial proteome. J Proteomics 2011; 74:2522-35. [DOI: 10.1016/j.jprot.2011.04.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2011] [Revised: 03/27/2011] [Accepted: 04/13/2011] [Indexed: 11/28/2022]
|
29
|
Della Corte A, Tamburrelli C, Crescente M, Giordano L, D'Imperio M, Di Michele M, Donati MB, De Gaetano G, Rotilio D, Cerletti C. Platelet proteome in healthy volunteers who smoke. Platelets 2011; 23:91-105. [PMID: 21736419 DOI: 10.3109/09537104.2011.587916] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Smoking accelerates atherosclerosis and is a well-known risk factor for acute cardiovascular complications; however, the mechanisms of these effects have not been completely clarified. Recently developed proteomic approaches may offer new clues when combined with well-established functional tests. Platelet proteome of healthy smokers and non-smokers was resolved by two-dimensional difference gel electrophoresis, compared by Decyder software and identified by mass spectrometry analysis (nano-LC-MS/MS). In smokers, three proteins (Factor XIII-A subunit, platelet glycoprotein IIb and beta-actin) were significantly up-regulated, whereas WDR1 protein and chaperonine HSP60 were down-regulated. Furthermore, the highest scored network derived by Ingenuity Pathway Analysis using the modulated proteins as input showed the involvement of several proteins to be related to inflammation and apoptosis. Platelet function tests and the levels of markers of platelet and leukocyte activation were not different in smokers vs. non-smoker subjects. The platelet proteomic approach confirms that cigarette smoking triggers several inflammatory reactions and may help clarify some of the molecular mechanisms of smoke effect on cellular systems relevant for vascular integrity and human health.
Collapse
Affiliation(s)
- Anna Della Corte
- Laboratory of Analytical Techniques and Proteomics, Research Laboratories, Catholic University, Campobasso, Italy.
| | | | | | | | | | | | | | | | | | | |
Collapse
|