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Shaba E, Landi C, Marzocchi C, Vantaggiato L, Bini L, Ricci C, Cantara S. Proteomics Reveals How the Tardigrade Damage Suppressor Protein Teaches Transfected Human Cells to Survive UV-C Stress. Int J Mol Sci 2023; 24:11463. [PMID: 37511223 PMCID: PMC10380570 DOI: 10.3390/ijms241411463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/12/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
The genome sequencing of the tardigrade Ramazzottius varieornatus revealed a unique nucleosome-binding protein named damage suppressor (Dsup), which was discovered to be crucial for the extraordinary abilities of tardigrades in surviving extreme stresses, such as UV. Evidence in Dsup-transfected human cells suggests that Dsup mediates an overall response in DNA damage signaling, DNA repair, and cell cycle regulation, resulting in an acquired resistance to stress. Given these promising outcomes, our study attempts to provide a wider comprehension of the molecular mechanisms modulated by Dsup in human cells and to explore the Dsup-activated molecular pathways under stress. We performed a differential proteomic analysis of Dsup-transfected and control human cells under basal conditions and at 24 h recovery after exposure to UV-C. We demonstrate via enrichment and network analyses, for the first time, that even in the absence of external stimuli, and more significantly, after stress, Dsup activates mechanisms involved with the unfolded protein response, the mRNA processing and stability, cytoplasmic stress granules, the DNA damage response, and the telomere maintenance. In conclusion, our results shed new light on Dsup-mediated protective mechanisms and increases our knowledge of the molecular machineries of extraordinary protection against UV-C stress.
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Affiliation(s)
- Enxhi Shaba
- Functional Proteomics Lab, Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Claudia Landi
- Functional Proteomics Lab, Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Carlotta Marzocchi
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy
| | - Lorenza Vantaggiato
- Functional Proteomics Lab, Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Luca Bini
- Functional Proteomics Lab, Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Claudia Ricci
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy
| | - Silvia Cantara
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy
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Bonente D, Bianchi L, De Salvo R, Nicoletti C, De Benedetto E, Bacci T, Bini L, Inzalaco G, Franci L, Chiariello M, Tosi GM, Bertelli E, Barone V. Co-Expression of Podoplanin and CD44 in Proliferative Vitreoretinopathy Epiretinal Membranes. Int J Mol Sci 2023; 24:ijms24119728. [PMID: 37298679 DOI: 10.3390/ijms24119728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023] Open
Abstract
Epiretinal membranes (ERMs) are sheets of tissue that pathologically develop in the vitreoretinal interface leading to progressive vision loss. They are formed by different cell types and by an exuberant deposition of extracellular matrix proteins. Recently, we reviewed ERMs' extracellular matrix components to better understand molecular dysfunctions that trigger and fuel the onset and development of this disease. The bioinformatics approach we applied delineated a comprehensive overview on this fibrocellular tissue and on critical proteins that could really impact ERM physiopathology. Our interactomic analysis proposed the hyaluronic-acid-receptor cluster of differentiation 44 (CD44) as a central regulator of ERM aberrant dynamics and progression. Interestingly, the interaction between CD44 and podoplanin (PDPN) was shown to promote directional migration in epithelial cells. PDPN is a glycoprotein overexpressed in various cancers and a growing body of evidence indicates its relevant function in several fibrotic and inflammatory pathologies. The binding of PDPN to partner proteins and/or its ligand results in the modulation of signaling pathways regulating proliferation, contractility, migration, epithelial-mesenchymal transition, and extracellular matrix remodeling, all processes that are vital in ERM formation. In this context, the understanding of the PDPN role can help to modulate signaling during fibrosis, hence opening a new line of therapy.
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Affiliation(s)
- Denise Bonente
- Department of Life Sciences, University of Siena, Via A. Moro 2, 53100 Siena, Italy
- Department of Molecular and Developmental Medicine, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Laura Bianchi
- Section of Functional Proteomics, Department of Life Sciences, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Rossana De Salvo
- Section of Functional Proteomics, Department of Life Sciences, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Claudio Nicoletti
- Department of Molecular and Developmental Medicine, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Elena De Benedetto
- Department of Medicine, Surgery and Neuroscience, University of Siena, Viale Mario Bracci 16, 53100 Siena, Italy
| | - Tommaso Bacci
- Department of Medicine, Surgery and Neuroscience, University of Siena, Viale Mario Bracci 16, 53100 Siena, Italy
| | - Luca Bini
- Section of Functional Proteomics, Department of Life Sciences, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Giovanni Inzalaco
- Core Research Laboratory (CRL), Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Via Fiorentina 1, 53100 Siena, Italy
- Istituto di Fisiologia Clinica (IFC), Consiglio Nazionale delle Ricerche (CNR), Via Fiorentina 1, 53100 Siena, Italy
- Department of Medical Biotechnologies, University of Siena, Viale Mario Bracci 16, 53100 Siena, Italy
| | - Lorenzo Franci
- Core Research Laboratory (CRL), Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Via Fiorentina 1, 53100 Siena, Italy
- Istituto di Fisiologia Clinica (IFC), Consiglio Nazionale delle Ricerche (CNR), Via Fiorentina 1, 53100 Siena, Italy
| | - Mario Chiariello
- Core Research Laboratory (CRL), Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Via Fiorentina 1, 53100 Siena, Italy
- Istituto di Fisiologia Clinica (IFC), Consiglio Nazionale delle Ricerche (CNR), Via Fiorentina 1, 53100 Siena, Italy
| | - Gian Marco Tosi
- Department of Medicine, Surgery and Neuroscience, University of Siena, Viale Mario Bracci 16, 53100 Siena, Italy
| | - Eugenio Bertelli
- Department of Molecular and Developmental Medicine, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Virginia Barone
- Department of Molecular and Developmental Medicine, University of Siena, Via A. Moro 2, 53100 Siena, Italy
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Landi C, Liberatori G, Puccini M, Shaba E, Vantaggiato L, Vitolo S, Corsi I, Bini L. Proteomics coupled with AhR-reporter gene bioassay for human and environmental safety assessment of sewage sludge and hydrochar. Sci Total Environ 2023:164651. [PMID: 37277040 DOI: 10.1016/j.scitotenv.2023.164651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/09/2023] [Accepted: 06/01/2023] [Indexed: 06/07/2023]
Abstract
Today application of sewage sludge (SL) and hydrochar (HC) in agriculture is a common practice for soil conditioning and crop fertilization, however safety concerns for human and environmental health due to the presence of toxic compounds have recently been expressed. Our aim was to test the suitability of proteomics coupled with bioanalytical tools for unravelling mixture effects of these applications in human and environmental safety assessment. We conducted proteomic and bioinformatic analysis of cell cultures used in the DR-CALUX® bioassay to identify proteins differentially abundant after exposure to SL and the corresponding HC, rather than only using the Bioanalytical Toxicity Equivalents (BEQs) obtained by DR-CALUX®. DR-CALUX® cells exposed to SL or HC showed a differential pattern of protein abundance depending on the type of SL and HC extract. The modified proteins are involved in antioxidant pathways, unfolded protein response and DNA damage that have close correlations with the effects of dioxin on biological systems and with onset of cancer and neurological disorders. Other cell response evidence suggested enrichment of heavy metals in the extracts. The present combined approach represents an advance in the application of bioanalytical tools for safety assessment of complex mixtures such as SL and HC. It proved successful in screening proteins, the abundance of which is determined by SL and HC and by the biological activity of legacy toxic compounds, including organohalogens.
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Affiliation(s)
- Claudia Landi
- Department of Life Sciences, University of Siena, Siena, Italy.
| | - Giulia Liberatori
- Department of Physical, Earth and Environmental Sciences, University of Siena, Siena, Italy
| | - Monica Puccini
- Department of Civil and Industrial Engineering, University of Pisa, Pisa, Italy
| | - Enxhi Shaba
- Department of Life Sciences, University of Siena, Siena, Italy
| | | | - Sandra Vitolo
- Department of Civil and Industrial Engineering, University of Pisa, Pisa, Italy
| | - Ilaria Corsi
- Department of Physical, Earth and Environmental Sciences, University of Siena, Siena, Italy
| | - Luca Bini
- Department of Life Sciences, University of Siena, Siena, Italy
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Vantaggiato L, Shaba E, Cameli P, Bergantini L, d’Alessandro M, Carleo A, Montuori G, Bini L, Bargagli E, Landi C. BAL Proteomic Signature of Lung Adenocarcinoma in IPF Patients and Its Transposition in Serum Samples for Less Invasive Diagnostic Procedures. Int J Mol Sci 2023; 24:ijms24020925. [PMID: 36674438 PMCID: PMC9861565 DOI: 10.3390/ijms24020925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a form of chronic and irreversible fibrosing interstitial pneumonia of unknown etiology. Although antifibrotic treatments have shown a reduction of lung function decline and a slow disease progression, IPF is characterize by a very high mortality. Emerging evidence suggests that IPF increases the risk of lung carcinogenesis. Both diseases show similarities in terms of risk factors, such as history of smoking, concomitant emphysema, and viral infections, besides sharing similar pathogenic pathways. Lung cancer (LC) diagnosis is often difficult in IPF patients because of the diffuse lung injuries and abnormalities due to the underlying fibrosis. This is reflected in the lack of optimal therapeutic strategies for patients with both diseases. For this purpose, we performed a proteomic study on bronchoalveolar lavage fluid (BALF) samples from IPF, LC associated with IPF (LC-IPF) patients, and healthy controls (CTRL). Molecular pathways involved in inflammation, immune response, lipid metabolism, and cell adhesion were found for the dysregulated proteins in LC-IPF, such as TTHY, APOA1, S10A9, RET4, GDIR1, and PROF1. The correlation test revealed a relationship between inflammation- and lipid metabolism-related proteins. PROF1 and S10A9, related to inflammation, were up-regulated in LC-IPF BAL and serum, while APOA1 and APOE linked to lipid metabolism, were highly abundant in IPF BAL and low abundant in IPF serum. Given the properties of cytokine/adipokine of the nicotinamide phosphoribosyltransferase, we also evaluated its serum abundance, highlighting its down-regulation in LC-IPF. Our retrospective analyses of BAL samples extrapolated some potential biomarkers of LC-IPF useful to improve the management of these contemporary pathologies. Their differential abundance in serum samples permits the measurement of these potential biomarkers with a less invasive procedure.
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Affiliation(s)
- Lorenza Vantaggiato
- Functional Proteomic Section, Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Enxhi Shaba
- Functional Proteomic Section, Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Paolo Cameli
- UOC Respiratory Diseases and Lung Transplantation, Department Internal and Specialist Medicine, University of Siena, 53100 Siena, Italy
| | - Laura Bergantini
- UOC Respiratory Diseases and Lung Transplantation, Department Internal and Specialist Medicine, University of Siena, 53100 Siena, Italy
| | - Miriana d’Alessandro
- UOC Respiratory Diseases and Lung Transplantation, Department Internal and Specialist Medicine, University of Siena, 53100 Siena, Italy
| | - Alfonso Carleo
- Department of Pneumology, Medical School Hannover (MHH), 30539 Hannover, Germany
| | - Giusy Montuori
- UOC Respiratory Diseases and Lung Transplantation, Department Internal and Specialist Medicine, University of Siena, 53100 Siena, Italy
| | - Luca Bini
- Functional Proteomic Section, Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Elena Bargagli
- UOC Respiratory Diseases and Lung Transplantation, Department Internal and Specialist Medicine, University of Siena, 53100 Siena, Italy
| | - Claudia Landi
- Functional Proteomic Section, Department of Life Sciences, University of Siena, 53100 Siena, Italy
- Correspondence:
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Vantaggiato L, Shaba E, Carleo A, Bezzini D, Pannuzzo G, Luddi A, Piomboni P, Bini L, Bianchi L. Neurodegenerative Disorder Risk in Krabbe Disease Carriers. Int J Mol Sci 2022; 23:ijms232113537. [PMID: 36362324 PMCID: PMC9654610 DOI: 10.3390/ijms232113537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/26/2022] [Accepted: 10/30/2022] [Indexed: 11/09/2022] Open
Abstract
Krabbe disease (KD) is a rare autosomal recessive disorder caused by mutations in the galactocerebrosidase gene (GALC). Defective GALC causes aberrant metabolism of galactolipids present almost exclusively in myelin, with consequent demyelinization and neurodegeneration of the central and peripheral nervous system (NS). KD shares some similar features with other neuropathies and heterozygous carriers of GALC mutations are emerging with an increased risk in developing NS disorders. In this work, we set out to identify possible variations in the proteomic profile of KD-carrier brain to identify altered pathways that may imbalance its homeostasis and that may be associated with neurological disorders. The differential analysis performed on whole brains from 33-day-old twitcher (galc −/−), heterozygous (galc +/−), and wild-type mice highlighted the dysregulation of several multifunctional factors in both heterozygous and twitcher mice. Notably, the KD-carrier mouse, despite its normal phenotype, presents the deregulation of vimentin, receptor of activated protein C kinase 1 (RACK1), myelin basic protein (MBP), 2′,3′-cyclic-nucleotide 3′-phosphodiesterase (CNP), transitional endoplasmic reticulum ATPase (VCP), and N-myc downstream regulated gene 1 protein (NDRG1) as well as changes in the ubiquitinated-protein pattern. Our findings suggest the carrier may be affected by dysfunctions classically associated with neurodegeneration: (i) alteration of (mechano) signaling and intracellular trafficking, (ii) a generalized affection of proteostasis and lipid metabolism, with possible defects in myelin composition and turnover, and (iii) mitochondrion and energy supply dysfunctions.
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Affiliation(s)
- Lorenza Vantaggiato
- Functional Proteomics Laboratory, Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Enxhi Shaba
- Functional Proteomics Laboratory, Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Alfonso Carleo
- Department of Pulmonology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Daiana Bezzini
- Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Giovanna Pannuzzo
- Department of Biochemical and Biotechnological Sciences, Section of Physiology, University of Catania, 95121 Catania, Italy
| | - Alice Luddi
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy
| | - Paola Piomboni
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy
| | - Luca Bini
- Functional Proteomics Laboratory, Department of Life Sciences, University of Siena, 53100 Siena, Italy
- Correspondence: ; Tel.: +39-0577-234938
| | - Laura Bianchi
- Functional Proteomics Laboratory, Department of Life Sciences, University of Siena, 53100 Siena, Italy
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Bianchi L, Altera A, Barone V, Bonente D, Bacci T, De Benedetto E, Bini L, Tosi GM, Galvagni F, Bertelli E. Untangling the Extracellular Matrix of Idiopathic Epiretinal Membrane: A Path Winding among Structure, Interactomics and Translational Medicine. Cells 2022; 11:cells11162531. [PMID: 36010606 PMCID: PMC9406781 DOI: 10.3390/cells11162531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 12/16/2022] Open
Abstract
Idiopathic epiretinal membranes (iERMs) are fibrocellular sheets of tissue that develop at the vitreoretinal interface. The iERMs consist of cells and an extracellular matrix (ECM) formed by a complex array of structural proteins and a large number of proteins that regulate cell–matrix interaction, matrix deposition and remodelling. Many components of the ECM tend to produce a layered pattern that can influence the tractional properties of the membranes. We applied a bioinformatics approach on a list of proteins previously identified with an MS-based proteomic analysis on samples of iERM to report the interactome of some key proteins. The performed pathway analysis highlights interactions occurring among ECM molecules, their cell receptors and intra- or extracellular proteins that may play a role in matrix biology in this special context. In particular, integrin β1, cathepsin B, epidermal growth factor receptor, protein-glutamine gamma-glutamyltransferase 2 and prolow-density lipoprotein receptor-related protein 1 are key hubs in the outlined protein–protein cross-talks. A section on the biomarkers that can be found in the vitreous humor of patients affected by iERM and that can modulate matrix deposition is also presented. Finally, translational medicine in iERM treatment has been summed up taking stock of the techniques that have been proposed for pharmacologic vitreolysis.
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Affiliation(s)
- Laura Bianchi
- Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Annalisa Altera
- Department of Life Sciences, University of Siena, 53100 Siena, Italy
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy
| | - Virginia Barone
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy
| | - Denise Bonente
- Department of Life Sciences, University of Siena, 53100 Siena, Italy
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy
| | - Tommaso Bacci
- Department of Medicine, Surgery and Neuroscience, University of Siena, 53100 Siena, Italy
| | - Elena De Benedetto
- Department of Medicine, Surgery and Neuroscience, University of Siena, 53100 Siena, Italy
| | - Luca Bini
- Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Gian Marco Tosi
- Department of Medicine, Surgery and Neuroscience, University of Siena, 53100 Siena, Italy
| | - Federico Galvagni
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Eugenio Bertelli
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy
- Correspondence:
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Shaba E, Vantaggiato L, Governini L, Haxhiu A, Sebastiani G, Fignani D, Grieco GE, Bergantini L, Bini L, Landi C. Multi-Omics Integrative Approach of Extracellular Vesicles: A Future Challenging Milestone. Proteomes 2022; 10:proteomes10020012. [PMID: 35645370 PMCID: PMC9149947 DOI: 10.3390/proteomes10020012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/14/2022] [Accepted: 04/19/2022] [Indexed: 02/01/2023] Open
Abstract
In the era of multi-omic sciences, dogma on singular cause-effect in physio-pathological processes is overcome and system biology approaches have been providing new perspectives to see through. In this context, extracellular vesicles (EVs) are offering a new level of complexity, given their role in cellular communication and their activity as mediators of specific signals to target cells or tissues. Indeed, their heterogeneity in terms of content, function, origin and potentiality contribute to the cross-interaction of almost every molecular process occurring in a complex system. Such features make EVs proper biological systems being, therefore, optimal targets of omic sciences. Currently, most studies focus on dissecting EVs content in order to either characterize it or to explore its role in various pathogenic processes at transcriptomic, proteomic, metabolomic, lipidomic and genomic levels. Despite valuable results being provided by individual omic studies, the categorization of EVs biological data might represent a limit to be overcome. For this reason, a multi-omic integrative approach might contribute to explore EVs function, their tissue-specific origin and their potentiality. This review summarizes the state-of-the-art of EVs omic studies, addressing recent research on the integration of EVs multi-level biological data and challenging developments in EVs origin.
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Affiliation(s)
- Enxhi Shaba
- Functional Proteomics Lab, Department of Life Sciences, University of Siena, 53100 Siena, Italy; (L.V.); (L.B.); (C.L.)
- Correspondence:
| | - Lorenza Vantaggiato
- Functional Proteomics Lab, Department of Life Sciences, University of Siena, 53100 Siena, Italy; (L.V.); (L.B.); (C.L.)
| | - Laura Governini
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy; (L.G.); (A.H.)
| | - Alesandro Haxhiu
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy; (L.G.); (A.H.)
| | - Guido Sebastiani
- Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; (G.S.); (D.F.); (G.E.G.)
- Fondazione Umberto Di Mario, c/o Toscana Life Sciences, 53100 Siena, Italy
| | - Daniela Fignani
- Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; (G.S.); (D.F.); (G.E.G.)
- Fondazione Umberto Di Mario, c/o Toscana Life Sciences, 53100 Siena, Italy
| | - Giuseppina Emanuela Grieco
- Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; (G.S.); (D.F.); (G.E.G.)
- Fondazione Umberto Di Mario, c/o Toscana Life Sciences, 53100 Siena, Italy
| | - Laura Bergantini
- Respiratory Diseases and Lung Transplant Unit, Department of Medical Sciences, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy;
| | - Luca Bini
- Functional Proteomics Lab, Department of Life Sciences, University of Siena, 53100 Siena, Italy; (L.V.); (L.B.); (C.L.)
| | - Claudia Landi
- Functional Proteomics Lab, Department of Life Sciences, University of Siena, 53100 Siena, Italy; (L.V.); (L.B.); (C.L.)
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Bianchi L, Casini S, Vantaggiato L, Di Noi A, Carleo A, Shaba E, Armini A, Bellucci F, Furii G, Bini L, Caliani I. A Novel Ex Vivo Approach Based on Proteomics and Biomarkers to Evaluate the Effects of Chrysene, MEHP, and PBDE-47 on Loggerhead Sea Turtles ( Caretta caretta). Int J Environ Res Public Health 2022; 19:ijerph19074369. [PMID: 35410049 PMCID: PMC8998652 DOI: 10.3390/ijerph19074369] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/18/2022] [Accepted: 04/02/2022] [Indexed: 02/04/2023]
Abstract
The principal aim of the present study was to develop and apply novel ex vivo tests as an alternative to cell cultures able to evaluate the possible effects of emerging and legacy contaminants in Caretta caretta. To this end, we performed ex vivo experiments on non-invasively collected whole-blood and skin-biopsy slices treated with chrysene, MEHP, or PBDE-47. Blood samples were tested by oxidative stress (TAS), immune system (respiratory burst, lysozyme, and complement system), and genotoxicity (ENA assay) biomarkers, and genotoxic and immune system effects were observed. Skin slices were analyzed by applying a 2D-PAGE/MS proteomic approach, and specific contaminant signatures were delineated on the skin proteomic profile. These reflect biochemical effects induced by each treatment and allowed to identify glutathione S-transferase P, peptidyl-prolyl cis-trans isomerase A, mimecan, and protein S100-A6 as potential biomarkers of the health-threatening impact the texted toxicants have on C. caretta. Obtained results confirm the suitability of the ex vivo system and indicate the potential risk the loggerhead sea turtle is undergoing in the natural environment. In conclusion, this work proved the relevance that the applied ex vivo models may have in testing the toxicity of other compounds and mixtures and in biomarker discovery.
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Affiliation(s)
- Laura Bianchi
- Functional Proteomics Laboratory, Department of Life Sciences, University of Siena, Via A. Moro, 2, 53100 Siena, Italy; (L.B.); (L.V.); (E.S.); (L.B.)
| | - Silvia Casini
- Department of Physical, Earth and Environmental Sciences, University of Siena, Via Mattioli, 4, 53100 Siena, Italy; (F.B.); (I.C.)
- Correspondence:
| | - Lorenza Vantaggiato
- Functional Proteomics Laboratory, Department of Life Sciences, University of Siena, Via A. Moro, 2, 53100 Siena, Italy; (L.B.); (L.V.); (E.S.); (L.B.)
| | - Agata Di Noi
- Department of Life Sciences, University of Siena, Via P. Mattioli, 4, 53100 Siena, Italy;
| | - Alfonso Carleo
- Department of Pulmonology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany;
| | - Enxhi Shaba
- Functional Proteomics Laboratory, Department of Life Sciences, University of Siena, Via A. Moro, 2, 53100 Siena, Italy; (L.B.); (L.V.); (E.S.); (L.B.)
| | - Alessandro Armini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro, 2, 53100 Siena, Italy;
| | - Francesco Bellucci
- Department of Physical, Earth and Environmental Sciences, University of Siena, Via Mattioli, 4, 53100 Siena, Italy; (F.B.); (I.C.)
| | - Giovanni Furii
- Centro Recupero Tartarughe Marine Legambiente, Molo di Ponente, 71043 Manfredonia, Italy;
| | - Luca Bini
- Functional Proteomics Laboratory, Department of Life Sciences, University of Siena, Via A. Moro, 2, 53100 Siena, Italy; (L.B.); (L.V.); (E.S.); (L.B.)
| | - Ilaria Caliani
- Department of Physical, Earth and Environmental Sciences, University of Siena, Via Mattioli, 4, 53100 Siena, Italy; (F.B.); (I.C.)
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Landi C, Liberatori G, Cotugno P, Sturba L, Vannuccini ML, Massari F, Miniero DV, Tursi A, Shaba E, Behnisch PA, Carleo A, Di Giuseppe F, Angelucci S, Bini L, Corsi I. First Attempt to Couple Proteomics with the AhR Reporter Gene Bioassay in Soil Pollution Monitoring and Assessment. Toxics 2021; 10:toxics10010009. [PMID: 35051051 PMCID: PMC8779689 DOI: 10.3390/toxics10010009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/22/2021] [Accepted: 12/24/2021] [Indexed: 11/16/2022]
Abstract
A topsoil sample obtained from a highly industrialized area (Taranto, Italy) was tested on the DR-CALUX® cell line and the exposed cells processed with proteomic and bioinformatics analyses. The presence of polyhalogenated compounds in the topsoil extracts was confirmed by GC-MS/MS analysis. Proteomic analysis of the cells exposed to the topsoil extracts identified 43 differential proteins. Enrichment analysis highlighted biological processes, such as the cellular response to a chemical stimulus, stress, and inorganic substances; regulation of translation; regulation of apoptotic process; and the response to organonitrogen compounds in light of particular drugs and compounds, extrapolated by bioinformatics all linked to the identified protein modifications. Our results confirm and reflect the complex epidemiological situation occurring among Taranto inhabitants and underline the need to further investigate the presence and sources of inferred chemicals in soils. The combination of bioassays and proteomics reveals a more complex scenario of chemicals able to affect cellular pathways and leading to toxicities rather than those identified by only bioassays and related chemical analysis. This combined approach turns out to be a promising tool for soil risk assessment and deserves further investigation and developments for soil monitoring and risk assessment.
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Affiliation(s)
- Claudia Landi
- Department of Life Sciences, University of Siena, 53100 Siena, Italy; (C.L.); (E.S.)
| | - Giulia Liberatori
- Department of Physical, Earth and Environmental Sciences, University of Siena, 53100 Siena, Italy; (G.L.); (L.S.); (M.L.V.)
| | - Pietro Cotugno
- Department of Biology, University of Bari Aldo Moro, 70121 Bari, Italy; (P.C.); (F.M.); (D.V.M.); (A.T.)
| | - Lucrezia Sturba
- Department of Physical, Earth and Environmental Sciences, University of Siena, 53100 Siena, Italy; (G.L.); (L.S.); (M.L.V.)
| | - Maria Luisa Vannuccini
- Department of Physical, Earth and Environmental Sciences, University of Siena, 53100 Siena, Italy; (G.L.); (L.S.); (M.L.V.)
| | - Federica Massari
- Department of Biology, University of Bari Aldo Moro, 70121 Bari, Italy; (P.C.); (F.M.); (D.V.M.); (A.T.)
| | - Daniela Valeria Miniero
- Department of Biology, University of Bari Aldo Moro, 70121 Bari, Italy; (P.C.); (F.M.); (D.V.M.); (A.T.)
| | - Angelo Tursi
- Department of Biology, University of Bari Aldo Moro, 70121 Bari, Italy; (P.C.); (F.M.); (D.V.M.); (A.T.)
| | - Enxhi Shaba
- Department of Life Sciences, University of Siena, 53100 Siena, Italy; (C.L.); (E.S.)
| | - Peter A. Behnisch
- BioDetection System BV (BDS) Amsterdam, 1098 XH Amsterdam, The Netherlands;
| | - Alfonso Carleo
- Department of Pulmonology, Hannover Medical School, 30625 Hannover, Germany;
| | - Fabrizio Di Giuseppe
- Department of Medical, Oral & Biotechnological Sciences, Dentistry and Biotechnology and Proteomics Unit, Centre of Advanced Studies and Technology, “G. D’Annunzio”, University of Chieti-Pescara, 66100 Chieti, Italy; (F.D.G.); (S.A.)
| | - Stefania Angelucci
- Department of Medical, Oral & Biotechnological Sciences, Dentistry and Biotechnology and Proteomics Unit, Centre of Advanced Studies and Technology, “G. D’Annunzio”, University of Chieti-Pescara, 66100 Chieti, Italy; (F.D.G.); (S.A.)
| | - Luca Bini
- Department of Life Sciences, University of Siena, 53100 Siena, Italy; (C.L.); (E.S.)
- Correspondence: (L.B.); (I.C.); Tel.: +39-0577-234938 (L.B.); +39-0577-232169 (I.C.)
| | - Ilaria Corsi
- Department of Physical, Earth and Environmental Sciences, University of Siena, 53100 Siena, Italy; (G.L.); (L.S.); (M.L.V.)
- Correspondence: (L.B.); (I.C.); Tel.: +39-0577-234938 (L.B.); +39-0577-232169 (I.C.)
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10
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Lanzafame M, Branca G, Landi C, Qiang M, Vaz B, Nardo T, Ferri D, Mura M, Iben S, Stefanini M, Peverali FA, Bini L, Orioli D. Cockayne syndrome group A and ferrochelatase finely tune ribosomal gene transcription and its response to UV irradiation. Nucleic Acids Res 2021; 49:10911-10930. [PMID: 34581821 PMCID: PMC8565352 DOI: 10.1093/nar/gkab819] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 08/10/2021] [Accepted: 09/12/2021] [Indexed: 11/14/2022] Open
Abstract
CSA and CSB proteins are key players in transcription-coupled nucleotide excision repair (TC-NER) pathway that removes UV-induced DNA lesions from the transcribed strands of expressed genes. Additionally, CS proteins play relevant but still elusive roles in other cellular pathways whose alteration may explain neurodegeneration and progeroid features in Cockayne syndrome (CS). Here we identify a CS-containing chromatin-associated protein complex that modulates rRNA transcription. Besides RNA polymerase I (RNAP1) and specific ribosomal proteins (RPs), the complex includes ferrochelatase (FECH), a well-known mitochondrial enzyme whose deficiency causes erythropoietic protoporphyria (EPP). Impairment of either CSA or FECH functionality leads to reduced RNAP1 occupancy on rDNA promoter that is associated to reduced 47S pre-rRNA transcription. In addition, reduced FECH expression leads to an abnormal accumulation of 18S rRNA that in primary dermal fibroblasts from CS and EPP patients results in opposed rRNA amounts. After cell irradiation with UV light, CSA triggers the dissociation of the CSA–FECH–CSB–RNAP1–RPs complex from the chromatin while it stabilizes its binding to FECH. Besides disclosing a function for FECH within nucleoli, this study sheds light on the still unknown mechanisms through which CSA modulates rRNA transcription.
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Affiliation(s)
- Manuela Lanzafame
- Institute of Molecular Genetics -L.L. Cavalli Sforza, CNR, 27100 Pavia, Italy
| | - Giulia Branca
- Institute of Molecular Genetics -L.L. Cavalli Sforza, CNR, 27100 Pavia, Italy
| | - Claudia Landi
- Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Mingyue Qiang
- Department of Dermatology and Allergic Diseases, Ulm University, Albert-Einstein Allee 23, 89081 Ulm, Germany
| | - Bruno Vaz
- Institute of Molecular Genetics -L.L. Cavalli Sforza, CNR, 27100 Pavia, Italy
| | - Tiziana Nardo
- Institute of Molecular Genetics -L.L. Cavalli Sforza, CNR, 27100 Pavia, Italy
| | - Debora Ferri
- Institute of Molecular Genetics -L.L. Cavalli Sforza, CNR, 27100 Pavia, Italy
| | - Manuela Mura
- Institute of Molecular Genetics -L.L. Cavalli Sforza, CNR, 27100 Pavia, Italy
| | - Sebastian Iben
- Department of Dermatology and Allergic Diseases, Ulm University, Albert-Einstein Allee 23, 89081 Ulm, Germany
| | - Miria Stefanini
- Institute of Molecular Genetics -L.L. Cavalli Sforza, CNR, 27100 Pavia, Italy
| | - Fiorenzo A Peverali
- Institute of Molecular Genetics -L.L. Cavalli Sforza, CNR, 27100 Pavia, Italy
| | - Luca Bini
- Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Donata Orioli
- Institute of Molecular Genetics -L.L. Cavalli Sforza, CNR, 27100 Pavia, Italy
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11
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Landi C, Vantaggiato L, Shaba E, Cameli P, Carleo A, d'Alessandro M, Bergantini L, Bargagli E, Bini L. Differential redox proteomic profiles of serum from severe asthma patients after one month of benralizumab and mepolizumab treatment. Pulm Pharmacol Ther 2021; 70:102060. [PMID: 34303823 DOI: 10.1016/j.pupt.2021.102060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/05/2021] [Accepted: 07/20/2021] [Indexed: 10/20/2022]
Abstract
Mepolizumab and Benralizumab are biological drugs for severe asthma patients able to reduce moderate-to-severe exacerbation rate (peripheral eosinophilial % mepolizumab 1.6 ± 1.2; benralizumab 0; p < 0.0001), improving the quality of life and lung function parameters (FEV1%: mepolizumab 87.1 ± 21.5; benralizumab 89.7 ± 15, p < 0.04). Here we report a preliminary redox proteomic study highlighting the level of oxidative burst present in serum from patients before and after one month of both treatments. Our results highlighted apolipoprotein A1 oxidation after Mepolizumab treatment, that could be related to HDL functionality and could represent a potential biomarker for the treatment. On the other hand, after one month of Benralizumab we detected higher oxidation levels of ceruloplasmin and transthyretin, considered an important oxidative stress biomarker which action help to maintain redox homeostasis.
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Affiliation(s)
- C Landi
- Functional Proteomics Lab, Department of Life Sciences, University of Siena, Siena, Italy.
| | - L Vantaggiato
- Functional Proteomics Lab, Department of Life Sciences, University of Siena, Siena, Italy
| | - E Shaba
- Functional Proteomics Lab, Department of Life Sciences, University of Siena, Siena, Italy
| | - P Cameli
- UOC Respiratory Diseases and Lung Transplantation, Department Internal and Specialist Medicine, University of Siena, Siena, Italy
| | - A Carleo
- Department of Pulmonology, Hannover Medical School, Hannover, Germany
| | - M d'Alessandro
- UOC Respiratory Diseases and Lung Transplantation, Department Internal and Specialist Medicine, University of Siena, Siena, Italy
| | - L Bergantini
- UOC Respiratory Diseases and Lung Transplantation, Department Internal and Specialist Medicine, University of Siena, Siena, Italy
| | - E Bargagli
- UOC Respiratory Diseases and Lung Transplantation, Department Internal and Specialist Medicine, University of Siena, Siena, Italy
| | - L Bini
- Functional Proteomics Lab, Department of Life Sciences, University of Siena, Siena, Italy
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12
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Bianchi L, Sframeli M, Vantaggiato L, Vita GL, Ciranni A, Polito F, Oteri R, Gitto E, Di Giuseppe F, Angelucci S, Versaci A, Messina S, Vita G, Bini L, Aguennouz M. Nusinersen Modulates Proteomics Profiles of Cerebrospinal Fluid in Spinal Muscular Atrophy Type 1 Patients. Int J Mol Sci 2021; 22:ijms22094329. [PMID: 33919289 PMCID: PMC8122268 DOI: 10.3390/ijms22094329] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 04/19/2021] [Indexed: 02/06/2023] Open
Abstract
Spinal muscular atrophy (SMA) type 1 is a severe infantile autosomal-recessive neuromuscular disorder caused by a survival motor neuron 1 gene (SMN1) mutation and characterized by progressive muscle weakness. Without supportive care, SMA type 1 is rapidly fatal. The antisense oligonucleotide nusinersen has recently improved the natural course of this disease. Here, we investigated, with a functional proteomic approach, cerebrospinal fluid (CSF) protein profiles from SMA type 1 patients who underwent nusinersen administration to clarify the biochemical response to the treatment and to monitor disease progression based on therapy. Six months after starting treatment (12 mg/5 mL × four doses of loading regimen administered at days 0, 14, 28, and 63), we observed a generalized reversion trend of the CSF protein pattern from our patient cohort to that of control donors. Notably, a marked up-regulation of apolipoprotein A1 and apolipoprotein E and a consistent variation in transthyretin proteoform occurrence were detected. Since these multifunctional proteins are critically active in biomolecular processes aberrant in SMA, i.e., synaptogenesis and neurite growth, neuronal survival and plasticity, inflammation, and oxidative stress control, their nusinersen induced modulation may support SMN improved-expression effects. Hence, these lipoproteins and transthyretin could represent valuable biomarkers to assess patient responsiveness and disease progression.
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Affiliation(s)
- Laura Bianchi
- Functional Proteomics Laboratory, Department of Life Sciences, University of Siena, 53100 Siena, Italy; (L.B.); (L.V.); (L.B.)
| | - Maria Sframeli
- Nemo Sud Clinical Centre, 98125 Messina, Italy; (M.S.); (G.L.V.)
| | - Lorenza Vantaggiato
- Functional Proteomics Laboratory, Department of Life Sciences, University of Siena, 53100 Siena, Italy; (L.B.); (L.V.); (L.B.)
| | - Gian Luca Vita
- Nemo Sud Clinical Centre, 98125 Messina, Italy; (M.S.); (G.L.V.)
| | - Annamaria Ciranni
- Unit of Neurology and Neuromuscular Diseases, Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy; (A.C.); (F.P.); (R.O.); (S.M.); (M.A.)
| | - Francesca Polito
- Unit of Neurology and Neuromuscular Diseases, Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy; (A.C.); (F.P.); (R.O.); (S.M.); (M.A.)
| | - Rosaria Oteri
- Unit of Neurology and Neuromuscular Diseases, Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy; (A.C.); (F.P.); (R.O.); (S.M.); (M.A.)
| | - Eloisa Gitto
- Neonatal and Paediatric Intensive Care Unit, Department of Human Pathology in Adult and Developmental Age, University of Messina, 98125 Messina, Italy;
| | - Fabrizio Di Giuseppe
- Dentistry and Biotechnology, and Proteomics Unit, Centre of Advanced Studies and Technoloy, Department Medical, Oral & Biotechnological Sciences, “G. d’Annunzio”, University of Chieti-Pescara, 66100 Chieti, Italy; (F.D.G.); (S.A.)
| | - Stefania Angelucci
- Dentistry and Biotechnology, and Proteomics Unit, Centre of Advanced Studies and Technoloy, Department Medical, Oral & Biotechnological Sciences, “G. d’Annunzio”, University of Chieti-Pescara, 66100 Chieti, Italy; (F.D.G.); (S.A.)
| | - Antonio Versaci
- Intensive Care Unit, AOU Policlinico “G. Martino”, 98125 Messina, Italy;
| | - Sonia Messina
- Unit of Neurology and Neuromuscular Diseases, Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy; (A.C.); (F.P.); (R.O.); (S.M.); (M.A.)
| | - Giuseppe Vita
- Nemo Sud Clinical Centre, 98125 Messina, Italy; (M.S.); (G.L.V.)
- Unit of Neurology and Neuromuscular Diseases, Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy; (A.C.); (F.P.); (R.O.); (S.M.); (M.A.)
- Correspondence:
| | - Luca Bini
- Functional Proteomics Laboratory, Department of Life Sciences, University of Siena, 53100 Siena, Italy; (L.B.); (L.V.); (L.B.)
| | - M’hammed Aguennouz
- Unit of Neurology and Neuromuscular Diseases, Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy; (A.C.); (F.P.); (R.O.); (S.M.); (M.A.)
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13
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Scali M, Moscatelli A, Bini L, Onelli E, Vignani R, Wang W. Protein Analysis of Pollen Tubes after the Treatments of Membrane Trafficking Inhibitors Gains Insights on Molecular Mechanism Underlying Pollen Tube Polar Growth. Protein J 2021; 40:205-222. [PMID: 33751342 PMCID: PMC8019430 DOI: 10.1007/s10930-021-09972-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2021] [Indexed: 12/03/2022]
Abstract
Pollen tube elongation is characterized by a highly-polarized tip growth process dependent on an efficient vesicular transport system and largely mobilized by actin cytoskeleton. Pollen tubes are an ideal model system to study exocytosis, endocytosis, membrane recycling, and signaling network coordinating cellular processes, structural organization and vesicular trafficking activities required for tip growth. Proteomic analysis was applied to identify Nicotiana tabacum Differentially Abundant Proteins (DAPs) after in vitro pollen tube treatment with membrane trafficking inhibitors Brefeldin A, Ikarugamycin and Wortmannin. Among roughly 360 proteins separated in two-dimensional gel electrophoresis, a total of 40 spots visibly changing between treated and control samples were identified by MALDI-TOF MS and LC-ESI-MS/MS analysis. The identified proteins were classified according to biological processes, and most proteins were related to pollen tube energy metabolism, including ammino acid synthesis and lipid metabolism, structural features of pollen tube growth as well modification and actin cytoskeleton organization, stress response, and protein degradation. In-depth analysis of proteins corresponding to energy-related pathways revealed the male gametophyte to be a reliable model of energy reservoir and dynamics.
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Affiliation(s)
- Monica Scali
- Department of Life Sciences, University of Siena, Siena, Italy.
| | | | - Luca Bini
- Department of Life Sciences, University of Siena, Siena, Italy
| | | | - Rita Vignani
- Department of Life Sciences, University of Siena, Siena, Italy
| | - Wei Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
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14
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Zanella I, König E, Tomasi M, Gagliardi A, Frattini L, Fantappiè L, Irene C, Zerbini F, Caproni E, Isaac SJ, Grigolato M, Corbellari R, Valensin S, Ferlenghi I, Giusti F, Bini L, Ashhab Y, Grandi A, Grandi G. Proteome-minimized outer membrane vesicles from Escherichia coli as a generalized vaccine platform. J Extracell Vesicles 2021; 10:e12066. [PMID: 33643549 PMCID: PMC7886703 DOI: 10.1002/jev2.12066] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 12/26/2020] [Accepted: 01/13/2021] [Indexed: 02/01/2023] Open
Abstract
Because of their potent adjuvanticity, ease of manipulation and simplicity of production Gram‐negative Outer Membrane Vesicles OMVs have the potential to become a highly effective vaccine platform. However, some optimization is required, including the reduction of the number of endogenous proteins, the increase of the loading capacity with respect to heterologous antigens, the enhancement of productivity in terms of number of vesicles per culture volume. In this work we describe the use of Synthetic Biology to create Escherichia coli BL21(DE3)Δ60, a strain releasing OMVs (OMVsΔ60) deprived of 59 endogenous proteins. The strain produces large quantities of vesicles (> 40 mg/L under laboratory conditions), which can accommodate recombinant proteins to a level ranging from 5% to 30% of total OMV proteins. Moreover, also thanks to the absence of immune responses toward the inactivated endogenous proteins, OMVsΔ60 decorated with heterologous antigens/epitopes elicit elevated antigens/epitopes‐specific antibody titers and high frequencies of epitope‐specific IFN‐γ‐producing CD8+ T cells. Altogether, we believe that E. coli BL21(DE3)Δ60 have the potential to become a workhorse factory for novel OMV‐based vaccines.
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Affiliation(s)
- Ilaria Zanella
- Department of Cellular, Computational and Integrative Biology (CIBIO) Laboratory of Synthetic and Structural Vaccinology University of Trento Trento Italy
| | - Enrico König
- Department of Cellular, Computational and Integrative Biology (CIBIO) Laboratory of Synthetic and Structural Vaccinology University of Trento Trento Italy
| | - Michele Tomasi
- Department of Cellular, Computational and Integrative Biology (CIBIO) Laboratory of Synthetic and Structural Vaccinology University of Trento Trento Italy
| | - Assunta Gagliardi
- Department of Cellular, Computational and Integrative Biology (CIBIO) Laboratory of Synthetic and Structural Vaccinology University of Trento Trento Italy
| | - Luca Frattini
- Department of Cellular, Computational and Integrative Biology (CIBIO) Laboratory of Synthetic and Structural Vaccinology University of Trento Trento Italy
| | | | - Carmela Irene
- Department of Cellular, Computational and Integrative Biology (CIBIO) Laboratory of Synthetic and Structural Vaccinology University of Trento Trento Italy
| | - Francesca Zerbini
- Department of Cellular, Computational and Integrative Biology (CIBIO) Laboratory of Synthetic and Structural Vaccinology University of Trento Trento Italy
| | - Elena Caproni
- Department of Cellular, Computational and Integrative Biology (CIBIO) Laboratory of Synthetic and Structural Vaccinology University of Trento Trento Italy
| | - Samine J Isaac
- Department of Cellular, Computational and Integrative Biology (CIBIO) Laboratory of Synthetic and Structural Vaccinology University of Trento Trento Italy
| | - Martina Grigolato
- Department of Cellular, Computational and Integrative Biology (CIBIO) Laboratory of Synthetic and Structural Vaccinology University of Trento Trento Italy
| | - Riccardo Corbellari
- Department of Cellular, Computational and Integrative Biology (CIBIO) Laboratory of Synthetic and Structural Vaccinology University of Trento Trento Italy
| | | | | | | | - Luca Bini
- Department of Life Sciences Functional Proteomics Laboratories University of Siena Siena Italy
| | - Yaqoub Ashhab
- Palestine-Korea Biotechnology Center Palestine Polytechnic University Hebron Palestine
| | - Alberto Grandi
- Toscana Life Sciences Foundation Siena Italy.,BiOMViS Srl Siena Italy
| | - Guido Grandi
- Department of Cellular, Computational and Integrative Biology (CIBIO) Laboratory of Synthetic and Structural Vaccinology University of Trento Trento Italy
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15
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Riva V, Garbelli A, Casiraghi F, Arena F, Trivisani CI, Gagliardi A, Bini L, Schroeder M, Maffia A, Sabbioneda S, Maga G. Novel alternative ribonucleotide excision repair pathways in human cells by DDX3X and specialized DNA polymerases. Nucleic Acids Res 2021; 48:11551-11565. [PMID: 33137198 PMCID: PMC7672437 DOI: 10.1093/nar/gkaa948] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 10/02/2020] [Accepted: 10/08/2020] [Indexed: 01/02/2023] Open
Abstract
Removal of ribonucleotides (rNMPs) incorporated into the genome by the ribonucleotide excision repair (RER) is essential to avoid genetic instability. In eukaryotes, the RNaseH2 is the only known enzyme able to incise 5' of the rNMP, starting the RER process, which is subsequently carried out by replicative DNA polymerases (Pols) δ or ϵ, together with Flap endonuclease 1 (Fen-1) and DNA ligase 1. Here, we show that the DEAD-box RNA helicase DDX3X has RNaseH2-like activity and can support fully reconstituted in vitro RER reactions, not only with Pol δ but also with the repair Pols β and λ. Silencing of DDX3X causes accumulation of rNMPs in the cellular genome. These results support the existence of alternative RER pathways conferring high flexibility to human cells in responding to the threat posed by rNMPs incorporation.
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Affiliation(s)
- Valentina Riva
- Institute of Molecular Genetics IGM-CNR 'Luigi Luca Cavalli-Sforza', via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Anna Garbelli
- Institute of Molecular Genetics IGM-CNR 'Luigi Luca Cavalli-Sforza', via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Federica Casiraghi
- Institute of Molecular Genetics IGM-CNR 'Luigi Luca Cavalli-Sforza', via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Francesca Arena
- Institute of Molecular Genetics IGM-CNR 'Luigi Luca Cavalli-Sforza', via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Claudia Immacolata Trivisani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. De Gasperi 2, I-53100 Siena, Italy
| | - Assunta Gagliardi
- Department of Life Sciences, Via A. Moro 2, University of Siena, I-53100 Siena, Italy
| | - Luca Bini
- Department of Life Sciences, Via A. Moro 2, University of Siena, I-53100 Siena, Italy
| | - Martina Schroeder
- Kathleen Lonsdale Institute for Human Health Research, Biology Department, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Antonio Maffia
- Institute of Molecular Genetics IGM-CNR 'Luigi Luca Cavalli-Sforza', via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Simone Sabbioneda
- Institute of Molecular Genetics IGM-CNR 'Luigi Luca Cavalli-Sforza', via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Giovanni Maga
- Institute of Molecular Genetics IGM-CNR 'Luigi Luca Cavalli-Sforza', via Abbiategrasso 207, I-27100 Pavia, Italy
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16
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Landi C, Cameli P, Vantaggiato L, Bergantini L, d'Alessandro M, Perruzza M, Carleo A, Shaba E, Di Giuseppe F, Angelucci S, Bargagli E, Bini L. Ceruloplasmin and oxidative stress in severe eosinophilic asthma patients treated with Mepolizumab and Benralizumab. Biochim Biophys Acta Proteins Proteom 2020; 1869:140563. [PMID: 33176218 DOI: 10.1016/j.bbapap.2020.140563] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/16/2020] [Accepted: 11/05/2020] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Severe eosinophilic asthma has been associated with Th2 airway inflammation and elevated proinflammatory cytokines and chemokines, such as IL-5. Precision therapies have recently been shown to improve asthma symptoms with a steroid-sparing effect. Two such therapies, Benralizumab and Mepolizumab, humanized IgG antibodies directed against the IL-5 receptor and IL-5, have been approved for severe eosinophilic asthma. METHODS Here we used a differential proteomic approach to analyse serum from patients with severe eosinophilic asthma treated with Benralizumab and Mepolizumab in a search for differential molecular modifications responsible of their effects. Enrichment analysis of differential proteins was performed for the two treatments. RESULTS AND DISCUSSION After one month of Benralizumab treatment we detected up-regulation of certain protein species of the antioxidant ceruloplasmin. To investigate oxidative stress, we performed redox proteomics which detected lower oxidative burst after one month of Benralizumab treatment than in the pre-treatment phase or after one month of Mepolizumab therapy.
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Affiliation(s)
- Claudia Landi
- Functional Proteomics Lab, Department of Life Sciences, University of Siena, Siena, Italy; UOC Respiratory Diseases and Lung Transplantation, Department Internal and Specialist Medicine, University of Siena, Siena, Italy
| | - Paolo Cameli
- UOC Respiratory Diseases and Lung Transplantation, Department Internal and Specialist Medicine, University of Siena, Siena, Italy
| | - Lorenza Vantaggiato
- Functional Proteomics Lab, Department of Life Sciences, University of Siena, Siena, Italy
| | - Laura Bergantini
- UOC Respiratory Diseases and Lung Transplantation, Department Internal and Specialist Medicine, University of Siena, Siena, Italy
| | - Miriana d'Alessandro
- UOC Respiratory Diseases and Lung Transplantation, Department Internal and Specialist Medicine, University of Siena, Siena, Italy
| | - Marco Perruzza
- UOC Respiratory Diseases and Lung Transplantation, Department Internal and Specialist Medicine, University of Siena, Siena, Italy
| | - Alfonso Carleo
- Department of Pulmonology, Hannover Medical School, Hannover, Germany
| | - Enxhi Shaba
- Functional Proteomics Lab, Department of Life Sciences, University of Siena, Siena, Italy
| | - Fabrizio Di Giuseppe
- Dept. Medical, Oral & Biotechnological Sciences, Dentistry and Biotechnology, and Proteomics Unit, Centre of Advanced Studies and Technoloy, "G. d'Annunzio", University of Chieti-Pescara, Italy
| | - Stefania Angelucci
- Dept. Medical, Oral & Biotechnological Sciences, Dentistry and Biotechnology, and Proteomics Unit, Centre of Advanced Studies and Technoloy, "G. d'Annunzio", University of Chieti-Pescara, Italy
| | - Elena Bargagli
- UOC Respiratory Diseases and Lung Transplantation, Department Internal and Specialist Medicine, University of Siena, Siena, Italy.
| | - Luca Bini
- Functional Proteomics Lab, Department of Life Sciences, University of Siena, Siena, Italy
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17
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Gori Savellini G, Bini L, Gagliardi A, Anichini G, Gandolfo C, Prathyumnan S, Cusi MG. Ubiquitin and Not Only Unfolded Domains Drives Toscana Virus Non-Structural NSs Protein Degradation. Viruses 2020; 12:E1153. [PMID: 33053780 PMCID: PMC7601456 DOI: 10.3390/v12101153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/05/2020] [Accepted: 10/09/2020] [Indexed: 01/09/2023] Open
Abstract
The non-structural protein NSs of the Phenuiviridae family members appears to have a role in the host immunity escape. The stability of Toscana virus (TOSV) NSs protein was tested by a cycloheximide (CHX) chase approach on cells transfected with NSs deleted versions fused to a reporter gene. The presence of intrinsically disordered regions (IDRs) both at the C- and N-terminus appeared to affect the protein stability. Indeed, the NSsΔC and NSsΔN proteins were more stable than the wild-type NSs counterpart. Since TOSV NSs exerts its inhibitory function by triggering RIG-I for proteasomal degradation, the interaction of the ubiquitin system and TOSV NSs was further examined. Chase experiments with CHX and the proteasome inhibitor MG-132 demonstrated the involvement of the ubiquitin-proteasome system in controlling NSs protein amount expressed in the cells. The analysis of TOSV NSs by mass spectrometry allowed the direct identification of K104, K109, K154, K180, K244, K294, and K298 residues targeted for ubiquitination. Analysis of NSs K-mutants confirmed the presence and the important role of lysine residues located in the central and the C-terminal parts of the protein in controlling the NSs cellular level. Therefore, we directly demonstrated a new cellular pathway involved in controlling TOSV NSs fate and activity, and this opens the way to new investigations among more pathogenic viruses of the Phenuiviridae family.
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Affiliation(s)
- Gianni Gori Savellini
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (G.A.); (C.G.); (S.P.); (M.G.C.)
| | - Luca Bini
- Department of Life Sciences, University of Siena, 53100 Siena, Italy;
| | - Assunta Gagliardi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Laboratory of Synthetic and Structural Vaccinology, 38122 Trento, Italy;
| | - Gabriele Anichini
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (G.A.); (C.G.); (S.P.); (M.G.C.)
| | - Claudia Gandolfo
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (G.A.); (C.G.); (S.P.); (M.G.C.)
- S. Maria delle Scotte Hospital, V.le Bracci, 1, 53100 Siena, Italy
| | - Shibily Prathyumnan
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (G.A.); (C.G.); (S.P.); (M.G.C.)
| | - Maria Grazia Cusi
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (G.A.); (C.G.); (S.P.); (M.G.C.)
- S. Maria delle Scotte Hospital, V.le Bracci, 1, 53100 Siena, Italy
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18
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Bargagli E, Refini RM, d’Alessandro M, Bergantini L, Cameli P, Vantaggiato L, Bini L, Landi C. Metabolic Dysregulation in Idiopathic Pulmonary Fibrosis. Int J Mol Sci 2020; 21:ijms21165663. [PMID: 32784632 PMCID: PMC7461042 DOI: 10.3390/ijms21165663] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 02/06/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a fibroproliferative disorder limited to the lung. New findings, starting from our proteomics studies on IPF, suggest that systemic involvement with altered molecular mechanisms and metabolic disorder is an underlying cause of fibrosis. The role of metabolic dysregulation in the pathogenesis of IPF has not been extensively studied, despite a recent surge of interest. In particular, our studies on bronchoalveolar lavage fluid have shown that the renin–angiotensin–aldosterone system (RAAS), the hypoxia/oxidative stress response, and changes in iron and lipid metabolism are involved in onset of IPF. These processes appear to interact in an intricate manner and to be related to different fibrosing pathologies not directly linked to the lung environment. The disordered metabolism of carbohydrates, lipids, proteins and hormones has been documented in lung, liver, and kidney fibrosis. Correcting these metabolic alterations may offer a new strategy for treating fibrosis. This paper focuses on the role of metabolic dysregulation in the pathogenesis of IPF and is a continuation of our previous studies, investigating metabolic dysregulation as a new target for fibrosis therapy.
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Affiliation(s)
- Elena Bargagli
- Respiratory Diseases and Lung Transplant Unit, Department of Medical and Surgical Sciences and Neurosciences, University of Siena, 53100 Siena, Italy; (E.B.); (R.M.R.); (M.d.); (L.B.); (P.C.)
| | - Rosa Metella Refini
- Respiratory Diseases and Lung Transplant Unit, Department of Medical and Surgical Sciences and Neurosciences, University of Siena, 53100 Siena, Italy; (E.B.); (R.M.R.); (M.d.); (L.B.); (P.C.)
| | - Miriana d’Alessandro
- Respiratory Diseases and Lung Transplant Unit, Department of Medical and Surgical Sciences and Neurosciences, University of Siena, 53100 Siena, Italy; (E.B.); (R.M.R.); (M.d.); (L.B.); (P.C.)
| | - Laura Bergantini
- Respiratory Diseases and Lung Transplant Unit, Department of Medical and Surgical Sciences and Neurosciences, University of Siena, 53100 Siena, Italy; (E.B.); (R.M.R.); (M.d.); (L.B.); (P.C.)
| | - Paolo Cameli
- Respiratory Diseases and Lung Transplant Unit, Department of Medical and Surgical Sciences and Neurosciences, University of Siena, 53100 Siena, Italy; (E.B.); (R.M.R.); (M.d.); (L.B.); (P.C.)
| | - Lorenza Vantaggiato
- Functional Proteomics Lab, Department Life Sciences, University of Siena, 53100 Siena, Italy; (L.V.); (L.B.)
| | - Luca Bini
- Functional Proteomics Lab, Department Life Sciences, University of Siena, 53100 Siena, Italy; (L.V.); (L.B.)
| | - Claudia Landi
- Respiratory Diseases and Lung Transplant Unit, Department of Medical and Surgical Sciences and Neurosciences, University of Siena, 53100 Siena, Italy; (E.B.); (R.M.R.); (M.d.); (L.B.); (P.C.)
- Functional Proteomics Lab, Department Life Sciences, University of Siena, 53100 Siena, Italy; (L.V.); (L.B.)
- Correspondence: ; Tel.: +39-0577-234-937
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19
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Vantaggiato L, Perruzza M, Refini RM, Bergantini L, d'Alessandro M, Cameli P, Perruzza D, Bini L, Bargagli E, Landi C. Mepolizumab and Benralizumab in Severe Eosinophilic Asthma: Preliminary Results of a Proteomic Study. Lung 2020; 198:761-765. [PMID: 32691140 DOI: 10.1007/s00408-020-00379-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/07/2020] [Indexed: 01/01/2023]
Abstract
Benralizumab and mepolizumab are new therapies for severe eosinophilic asthma. They are both humanized IgG antibodies, targeting the IL-5 receptor and IL-5, respectively, suppressing the corresponding pathways. No specific biomarkers have been proposed to evaluate treatment response to benralizumab or mepolizumab. The aim of this proteomic study was to compare serum protein profiles of patients with severe eosinophilic asthma before and after anti-IL5 or anti-IL5R therapies. Proteomic analysis highlighted 22 differently abundant spots. Among the proteins identified, CAYP1, A1AT and A2M expression was significantly modified in both groups of patients after therapies while ceruloplasmin showed a significant modification in the group of benralizumab treatment. These differentially expressed proteins could be potential biomarkers of response to mepolizumab and benralizumab treatments and need further evaluation.
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Affiliation(s)
- Lorenza Vantaggiato
- Functional Proteomics Lab, Department of Life Sciences, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Marco Perruzza
- UOC Respiratory Diseases and Lung Transplantation, Department Internal and Specialist Medicine, University of Siena, Siena, Italy
| | - Rosa Metella Refini
- UOC Respiratory Diseases and Lung Transplantation, Department Internal and Specialist Medicine, University of Siena, Siena, Italy
| | - Laura Bergantini
- UOC Respiratory Diseases and Lung Transplantation, Department Internal and Specialist Medicine, University of Siena, Siena, Italy
| | - Miriana d'Alessandro
- UOC Respiratory Diseases and Lung Transplantation, Department Internal and Specialist Medicine, University of Siena, Siena, Italy
| | - Paolo Cameli
- UOC Respiratory Diseases and Lung Transplantation, Department Internal and Specialist Medicine, University of Siena, Siena, Italy
| | - Davide Perruzza
- Unit of Basic and Applied Biosciences, University of Teramo, Via Balzarini 1, 64100, Teramo, Italy
| | - Luca Bini
- Functional Proteomics Lab, Department of Life Sciences, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Elena Bargagli
- UOC Respiratory Diseases and Lung Transplantation, Department Internal and Specialist Medicine, University of Siena, Siena, Italy
| | - Claudia Landi
- Functional Proteomics Lab, Department of Life Sciences, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy. .,UOC Respiratory Diseases and Lung Transplantation, Department Internal and Specialist Medicine, University of Siena, Siena, Italy.
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20
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Landi C, Bergantini L, Cameli P, d'Alessandro M, Carleo A, Shaba E, Rottoli P, Bini L, Bargagli E. Idiopathic Pulmonary Fibrosis Serum proteomic analysis before and after nintedanib therapy. Sci Rep 2020; 10:9378. [PMID: 32523095 PMCID: PMC7287088 DOI: 10.1038/s41598-020-66296-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 05/16/2020] [Indexed: 11/30/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a fatal progressive disease with a median survival of 2–5 years. Nintedanib is a small tyrosine kinase inhibitor that reduces IPF progression, significantly slowing the annual decline in Forced Vital Capacity (FVC). Very little data is available on the molecular mechanisms of this treatment in IPF, despite a growing interest in the definition of IPF pathogenesis and target therapy. A functional proteomic approach was applied to the analysis of serum samples from IPF patients in order to highlight differential proteins potentially indicative of drug-induced molecular pathways modifications and response to therapy. Twelve serum samples were collected from six IPF patients in care at Siena Regional Referral Center for Interstitial Lung Diseases (ILDs) and treated with nintedanib for one year. Serum samples were analyzed at baseline (T0 before starting therapy) and after one year of treatment (T1) and underwent differential proteomic and bioinformatic analysis. Proteomic analysis revealed 13 protein species that were significantly increased after one year of treatment. When the targets of nintedanib (VEGFR, FGFR and PDGFR) were added, enrichment analysis extracted molecular pathways and process networks involved in cell differentiation (haptoglobin and albumin), coagulation (antithrombin III), epithelial mesenchymal transition, cell proliferation and transmigration. PI3K and MAPK induced up-regulation of apolipoprotein C3. Proteomic study found 13 protein species up-regulated in IPF patients after one year of nintedanib treatment. Haptoglobin, a central hub of our analysis was validated by 2D-WB and ELISA as theranostic marker in a more numerous populations of patients.
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Affiliation(s)
- Claudia Landi
- Functional Proteomics Lab, Dept. Life Sciences, University of Siena, Siena, Italy. .,Respiratory Diseases and Lung Transplant Unit, Dept. Internal and Specialist Medicine, AOUS, Siena, Italy.
| | - Laura Bergantini
- Respiratory Diseases and Lung Transplant Unit, Dept. Internal and Specialist Medicine, AOUS, Siena, Italy
| | - Paolo Cameli
- Respiratory Diseases and Lung Transplant Unit, Dept. Internal and Specialist Medicine, AOUS, Siena, Italy
| | - Miriana d'Alessandro
- Respiratory Diseases and Lung Transplant Unit, Dept. Internal and Specialist Medicine, AOUS, Siena, Italy
| | - Alfonso Carleo
- Department of Pneumology, Medical School Hannover (MHH), Hannover, Germany
| | - Enxhi Shaba
- Functional Proteomics Lab, Dept. Life Sciences, University of Siena, Siena, Italy
| | - Paola Rottoli
- Respiratory Diseases and Lung Transplant Unit, Dept. Internal and Specialist Medicine, AOUS, Siena, Italy
| | - Luca Bini
- Functional Proteomics Lab, Dept. Life Sciences, University of Siena, Siena, Italy
| | - Elena Bargagli
- Respiratory Diseases and Lung Transplant Unit, Dept. Internal and Specialist Medicine, AOUS, Siena, Italy
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21
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Bargagli E, Cameli P, Carleo A, Refini RM, Bergantini L, D'alessandro M, Vietri L, Perillo F, Volterrani L, Rottoli P, Bini L, Landi C. The effect of cigarette smoking on bronchoalveolar lavage protein profiles from patients with different interstitial lung diseases. Panminerva Med 2020; 62:109-115. [DOI: 10.23736/s0031-0808.19.03754-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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22
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Carleo A, Landi C, Prasse A, Bergantini L, D'Alessandro M, Cameli P, Janciauskiene S, Rottoli P, Bini L, Bargagli E. Proteomic characterization of idiopathic pulmonary fibrosis patients: stable versus acute exacerbation. Monaldi Arch Chest Dis 2020; 90. [PMID: 32362107 DOI: 10.4081/monaldi.2020.1231] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/10/2020] [Indexed: 11/23/2022] Open
Abstract
Acute exacerbations (AEs) are among the main causes of death in idiopathic pulmonary fibrosis (IPF) patients. In this study proteomic comparative analysis of bronchoalveolar lavage (BAL) fluid samples was performed in stable IPF patients versus AEs IPF group to identify AE pathogenetic mechanisms and novel potential predictive biomarkers. A functional proteomic analysis of BAL fluid samples from stable and AE-IPF patients was conducted in a population of 27 IPF patients. Fifty-one differentially abundant spots were observed and identified by mass spectrometry. Enrichment analysis found proteins of interest involved in the regulation of macrophages and lipid metabolism receptors. In acute exacerbation IPF group, differentially abundant proteins were involved in propagation of the β-catenin WNT transduction signal, and proteins up-regulated in lung carcinogenesis (IGKC, S100A9, PEDF, IGHG1, ALDOA, A1AT, HPT, CO3 and PIGR) and acute phase proteins involved in protease-antiprotease imbalance (such as A1AT fragments). Dot-blot analysis of A1AT C-36 peptide allowed validating our findings, confirming up-regulation in AE IPF patients and suggesting its potential pathogenetic role. A crucial role of protease/antiprotease imbalance, clathrin-mediated endocytosis signalling and carcinogenesis emerged in IPF patients developing acute exacerbations.
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Affiliation(s)
- Alfonso Carleo
- Department of Pneumology, Hannover Medical School (MHH), Hannover.
| | - Claudia Landi
- Functional Proteomic Section, Department of Life Sciences, University of Siena.
| | - Antje Prasse
- Department of Pneumology, Hannover Medical School (MHH), Hannover.
| | - Laura Bergantini
- Unit of Respiratory Diseases and Lung Transplantation, Department of Internal and Specialist Medicine, University of Siena.
| | - Miriana D'Alessandro
- Unit of Respiratory Diseases and Lung Transplantation, Department of Internal and Specialist Medicine, University of Siena.
| | - Paolo Cameli
- Unit of Respiratory Diseases and Lung Transplantation, Department of Internal and Specialist Medicine, University of Siena.
| | | | - Paola Rottoli
- Unit of Respiratory Diseases and Lung Transplantation, Department of Internal and Specialist Medicine, University of Siena.
| | - Luca Bini
- Functional Proteomic Section, Department of Life Sciences, University of Siena.
| | - Elena Bargagli
- Unit of Respiratory Diseases and Lung Transplantation, Department of Internal and Specialist Medicine, University of Siena.
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23
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Stroppa N, Onelli E, Hejna M, Rossi L, Gagliardi A, Bini L, Baldi A, Moscatelli A. Typha latifolia and Thelypteris palustris behavior in a pilot system for the refinement of livestock wastewaters: A case of study. Chemosphere 2020; 240:124915. [PMID: 31563105 DOI: 10.1016/j.chemosphere.2019.124915] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/18/2019] [Accepted: 09/18/2019] [Indexed: 06/10/2023]
Abstract
In animal livestock heavy metals are widely used as feed additives to control enteric bacterial infections as well as to enhance the integrity of the immune system. As these metals are only partially adsorbed by animals, the content of heavy metals in manure and wastewaters causes soil and ground water contamination, with Zn2+ and Cu2+ being the most critical output from pig livestock. Phytoremediation is considered a valid strategy to improve the purity of wastewaters. This work studied the effect of Zn2+ and Cu2+ on the morphology and protein expression in Thelypteris palustris and Typha latifolia plants, cultured in a wetland pilot system. Despite the absence of macroscopic alterations, remodeling of cell walls and changes in carbohydrate metabolism were observed in the rhizomes of both plants and in leaves of Thelypteris palustris. However, similar modifications seemed to be determined by the alterations of different mechanisms in these plants. These data also suggested that marsh ferns are more sensitive to metals than monocots. Whereas toleration mechanisms seemed to be activated in Typha latifolia, in Thelypteris palustris the observed modifications appeared as slight toxic effects due to metal exposure. This study clearly indicates that both plants could be successfully employed in in situ phytoremediation systems, to remove Cu2+ and Zn2+ at concentrations that are ten times higher than the legal limits, without affecting plant growth.
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Affiliation(s)
- Nadia Stroppa
- Department of Biosciences, University of Milano, Via Celoria 26, 20133, Milan, Italy.
| | - Elisabetta Onelli
- Department of Biosciences, University of Milano, Via Celoria 26, 20133, Milan, Italy.
| | - Monika Hejna
- Department of Health, Animal Science and Food Safety, University of Milano, Via Celoria 10, 20133, Milan, Italy.
| | - Luciana Rossi
- Department of Health, Animal Science and Food Safety, University of Milano, Via Celoria 10, 20133, Milan, Italy.
| | - Assunta Gagliardi
- Dipartimento di Biologia Cellulare, Computazionale e Integrata - CIBIO, University of Trento, Via Sommarive 9, Povo, 38123, Trento, Italy.
| | - Luca Bini
- Department of Life Science, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy.
| | - Antonella Baldi
- Department of Health, Animal Science and Food Safety, University of Milano, Via Celoria 10, 20133, Milan, Italy.
| | - Alessandra Moscatelli
- Department of Biosciences, University of Milano, Via Celoria 26, 20133, Milan, Italy.
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24
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Landi C, Luddi A, Bianchi L, Pannuzzo G, Pavone V, Piomboni P, Bini L. Proteostasis network alteration in lysosomal storage disorders: Insights from the mouse model of Krabbe disease. J Neurosci Res 2019; 98:718-733. [PMID: 31797419 DOI: 10.1002/jnr.24558] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/09/2019] [Accepted: 10/29/2019] [Indexed: 12/19/2022]
Abstract
In Krabbe disease, a mutation in GALC gene causes widespread demyelination determining cell death by apoptosis, mainly in oligodendrocytes and Schwann cells. Less is known on the molecular mechanisms induced by this deficiency. Here, we report an impairment in protein synthesis and degradation and in proteasomal clearance with a potential accumulation of the misfolded proteins and induction of the endoplasmic reticulum stress in the brain of 6-day-old twitcher mice (TM) (model of Krabbe disease). In particular, an imbalance of the immunoproteasome function was highlighted, useful for shaping adaptive immune response by neurological cells. Moreover, our data show an involvement of cytoskeleton remodeling in Krabbe pathogenesis, with a lamin meshwork disaggregation in twitcher oligodendrocytes in 6-day-old TM. This study provides interesting protein targets and mechanistic insight on the early onset of Krabbe disease that may be promising options to be tested in combination with currently available therapies to rescue Krabbe phenotype.
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Affiliation(s)
- Claudia Landi
- Department of Life Sciences, University of Siena, Siena, Italy
| | - Alice Luddi
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Laura Bianchi
- Department of Life Sciences, University of Siena, Siena, Italy
| | - Giovanna Pannuzzo
- Department of Biomedical and Biotechnological Sciences, Section of Physiology, University of Catania, Catania, Italy
| | - Valentina Pavone
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Paola Piomboni
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Luca Bini
- Department of Life Sciences, University of Siena, Siena, Italy
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25
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Alfano L, Caporaso A, Altieri A, Dell'Aquila M, Landi C, Bini L, Pentimalli F, Giordano A. Depletion of the RNA binding protein HNRNPD impairs homologous recombination by inhibiting DNA-end resection and inducing R-loop accumulation. Nucleic Acids Res 2019; 47:4068-4085. [PMID: 30799487 PMCID: PMC6486545 DOI: 10.1093/nar/gkz076] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 01/24/2019] [Accepted: 02/01/2019] [Indexed: 12/12/2022] Open
Abstract
DNA double strand break (DSB) repair through homologous recombination (HR) is crucial to maintain genome stability. DSB resection generates a single strand DNA intermediate, which is crucial for the HR process. We used a synthetic DNA structure, mimicking a resection intermediate, as a bait to identify proteins involved in this process. Among these, LC/MS analysis identified the RNA binding protein, HNRNPD. We found that HNRNPD binds chromatin, although this binding occurred independently of DNA damage. However, upon damage, HNRNPD re-localized to γH2Ax foci and its silencing impaired CHK1 S345 phosphorylation and the DNA end resection process. Indeed, HNRNPD silencing reduced: the ssDNA fraction upon camptothecin treatment; AsiSI-induced DSB resection; and RPA32 S4/8 phosphorylation. CRISPR/Cas9-mediated HNRNPD knockout impaired in vitro DNA resection and sensitized cells to camptothecin and olaparib treatment. We found that HNRNPD interacts with the heterogeneous nuclear ribonucleoprotein SAF-A previously associated with DNA damage repair. HNRNPD depletion resulted in an increased amount of RNA:DNA hybrids upon DNA damage. Both the expression of RNase H1 and RNA pol II inhibition recovered the ability to phosphorylate RPA32 S4/8 in HNRNPD knockout cells upon DNA damage, suggesting that RNA:DNA hybrid resolution likely rescues the defective DNA damage response of HNRNPD-depleted cells.
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Affiliation(s)
- Luigi Alfano
- Oncology Research Center of Mercogliano (CROM); Istituto Nazionale Tumori, IRCCS, Fondazione G. Pascale, Napoli, Italia
| | - Antonella Caporaso
- Department of Medical Biotechnologies, University of Siena, Siena, Italia.,Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA
| | - Angela Altieri
- Department of Medical Biotechnologies, University of Siena, Siena, Italia
| | - Milena Dell'Aquila
- Department of Medical Biotechnologies, University of Siena, Siena, Italia
| | - Claudia Landi
- Department of Life Sciences, University of Siena, Siena, Italia
| | - Luca Bini
- Department of Life Sciences, University of Siena, Siena, Italia
| | - Francesca Pentimalli
- Oncology Research Center of Mercogliano (CROM); Istituto Nazionale Tumori, IRCCS, Fondazione G. Pascale, Napoli, Italia
| | - Antonio Giordano
- Department of Medical Biotechnologies, University of Siena, Siena, Italia.,Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA
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26
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Parrotta L, Aloisi I, Suanno C, Faleri C, Kiełbowicz-Matuk A, Bini L, Cai G, Del Duca S. A low molecular-weight cyclophilin localizes in different cell compartments of Pyrus communis pollen and is released in vitro under Ca 2+ depletion. Plant Physiol Biochem 2019; 144:197-206. [PMID: 31585398 DOI: 10.1016/j.plaphy.2019.09.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/26/2019] [Accepted: 09/26/2019] [Indexed: 06/10/2023]
Abstract
Cyclophilins (CyPs) are ubiquitous proteins involved in a wide variety of processes including protein maturation and trafficking, receptor complex stabilization, apoptosis, receptor signaling, RNA processing, and spliceosome assembly. The ubiquitous presence is justified by their peptidyl-prolyl cis-trans isomerase (PPIase) activity, catalyzing the rotation of X-Pro peptide bonds from a cis to a trans conformation, a critical rate-limiting step in protein folding, as over 90% of proteins contain trans prolyl imide bonds. In Arabidopsis 35 CyPs involved in plant development have been reported, showing different subcellular localizations and tissue- and stage-specific expression. In the present work, we focused on the localization of CyPs in pear (Pyrus communis) pollen, a model system for studies on pollen tube elongation and on pollen-pistil self-incompatibility response. Fluorescent, confocal and immuno-electron microscopy showed that this protein is present in the cytoplasm, organelles and cell wall, as confirmed by protein fractionation. Moreover, an 18-kDa CyP isoform was specifically released extracellularly when pear pollen was incubated with the Ca2+ chelator EGTA.
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Affiliation(s)
- Luigi Parrotta
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Iris Aloisi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Chiara Suanno
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Claudia Faleri
- Department of Life Sciences, University of Siena, Siena, Italy
| | | | - Luca Bini
- Department of Life Sciences, University of Siena, Siena, Italy
| | - Giampiero Cai
- Department of Life Sciences, University of Siena, Siena, Italy
| | - Stefano Del Duca
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy.
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Landi C, Bargagli E, Carleo A, Refini RM, Bennett D, Bianchi L, Cillis G, Prasse A, Bini L, Rottoli P. Bronchoalveolar lavage proteomic analysis in pulmonary fibrosis associated with systemic sclerosis: S100A6 and 14-3-3ε as potential biomarkers. Rheumatology (Oxford) 2019; 58:165-178. [PMID: 30239835 DOI: 10.1093/rheumatology/key223] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Indexed: 11/14/2022] Open
Abstract
Objective SSc is a rare severe connective tissue disorder. Its prognosis is mainly related to the development of pulmonary fibrosis (PF)-SSc and pulmonary arterial hypertension. No known therapy for PF-SSc modifies progressive lung fibrotic involvement. Research is therefore aimed at a deeper understanding of complex pathogenetic mechanisms and the possibility of new prognostic biomarkers and therapeutic targets. Methods Towards the first of these aims, we conducted functional proteomic analysis of bronchoalveolar lavage samples from PF-SSc patients and smoker and non-smoker controls. Results The differential expression pattern revealed by principal component analysis highlighted a specific protein profile of PF-SSc with respect to control samples, and enrichment analysis shed light on process networks involved in pathogenesis. The proteins identified are known to be involved in lung inflammation of PF-SSc-induced IL6 signalling, the complement system, innate immunity, Jak-STAT, the kallikrein-kinin system, blood coagulation, the immune response mediated by phagocytosis and phagosomes in antigen presentation. In particular, our MetaCore network suggested C3a, APOAI, 14-3-3ε, SPFA2 and S100A6 as potential biomarkers; these are upstream molecules involved in lung fibrosis, innate immunity and vascular damage occurring in PF-SSc. Conclusion This report provides a molecular overview of pathological processes in PF-SSc, pinpointing possible new disease biomarkers and therapeutic targets.
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Affiliation(s)
- Claudia Landi
- Functional Proteomic Laboratory, Department of Life Sciences, University of Siena, Siena, Italy.,Respiratory Diseases and Lung Transplant Unit, Department of Internal and Specialist Medicine AOUS, University of Siena, Siena, Italy
| | - Elena Bargagli
- Respiratory Diseases and Lung Transplant Unit, Department of Internal and Specialist Medicine AOUS, University of Siena, Siena, Italy
| | - Alfonso Carleo
- Department of Pulmonology, Hannover Medical School, Hannover, Germany
| | - Rosa Metella Refini
- Respiratory Diseases and Lung Transplant Unit, Department of Internal and Specialist Medicine AOUS, University of Siena, Siena, Italy
| | - David Bennett
- Respiratory Diseases and Lung Transplant Unit, Department of Internal and Specialist Medicine AOUS, University of Siena, Siena, Italy
| | - Laura Bianchi
- Functional Proteomic Laboratory, Department of Life Sciences, University of Siena, Siena, Italy
| | - Giuseppe Cillis
- Respiratory Diseases and Lung Transplant Unit, Department of Internal and Specialist Medicine AOUS, University of Siena, Siena, Italy
| | - Antje Prasse
- Department of Pulmonology, Hannover Medical School, Hannover, Germany
| | - Luca Bini
- Functional Proteomic Laboratory, Department of Life Sciences, University of Siena, Siena, Italy
| | - Paola Rottoli
- Respiratory Diseases and Lung Transplant Unit, Department of Internal and Specialist Medicine AOUS, University of Siena, Siena, Italy
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Della Torre C, Maggioni D, Ghilardi A, Parolini M, Santo N, Landi C, Madaschi L, Magni S, Tasselli S, Ascagni M, Bini L, La Porta C, Del Giacco L, Binelli A. The interactions of fullerene C 60 and Benzo(α)pyrene influence their bioavailability and toxicity to zebrafish embryos. Environ Pollut 2018; 241:999-1008. [PMID: 30029334 DOI: 10.1016/j.envpol.2018.06.042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/13/2018] [Accepted: 06/13/2018] [Indexed: 06/08/2023]
Abstract
This study aimed to assess the toxicological consequences related to the interaction of fullerene nanoparticles (C60) and Benzo(α)pyrene (B(α)P) on zebrafish embryos, which were exposed to C60 and B(α)P alone and to C60 doped with B(α)P. The uptake of pollutants into their tissues and intra-cellular localization were investigated by immunofluorescence and electron microscopy. A set of biomarkers of genotoxicity and oxidative stress, as well as functional proteomics analysis were applied to assess the toxic effects due to C60 interaction with B(α)P. The carrier role of C60 for B(α)P was observed, however adsorption on C60 did not affect the accumulation and localization of B(α)P in the embryos. Instead, C60 doped with B(α)P resulted more prone to sedimentation and less bioavailable for the embryos compared to C60 alone. As for toxicity, our results suggested that C60 alone elicited oxidative stress in embryos and a down-regulation of proteins involved in energetic metabolism. The C60 + B(α)P induced cellular response mechanisms similar to B(α)P alone, but generating greater cellular damages in the exposed embryos.
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Affiliation(s)
| | | | - Anna Ghilardi
- Department of Biosciences, University of Milan, Italy
| | - Marco Parolini
- Department of Environmental Science and Policy, University of Milan, Italy
| | - Nadia Santo
- Department of Biosciences, University of Milan, Italy
| | - Claudia Landi
- Department of Life Science, University of Siena, Italy
| | | | - Stefano Magni
- Department of Biosciences, University of Milan, Italy
| | - Stefano Tasselli
- CNR-IRSA (National Research Council-Water Research Institute), Brugherio, Italy
| | | | - Luca Bini
- Department of Life Science, University of Siena, Italy
| | - Caterina La Porta
- Department of Environmental Science and Policy, University of Milan, Italy
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Binelli A, Magni S, La Porta C, Bini L, Della Torre C, Ascagni M, Maggioni D, Ghilardi A, Armini A, Landi C, Santo N, Madaschi L, Coccè V, Mutti F, Lionetti MC, Ciusani E, Del Giacco L. Cellular pathways affected by carbon nanopowder-benzo(α)pyrene complex in human skin fibroblasts identified by proteomics. Ecotoxicol Environ Saf 2018; 160:144-153. [PMID: 29803189 DOI: 10.1016/j.ecoenv.2018.05.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/09/2018] [Accepted: 05/11/2018] [Indexed: 06/08/2023]
Abstract
One of the crucial and unsolved problems of the airborne carbon nanoparticles is the role played by the adsorbed environmental pollutants on their toxicological effect. Indeed, in the urban areas, the carbon nanoparticles usually adsorb some atmospheric contaminants, whose one of the leading representatives is the benzo(α)pyrene. Herein, we used the proteomics to investigate the alteration of toxicological pathways due to the carbon nanopowder-benzo(α)pyrene complex in comparison with the two contaminants administered alone on human skin-derived fibroblasts (hSDFs) exposed for 8 days in semi-static conditions. The preliminary confocal microscopy observations highlighted that carbon-nanopowder was able to pass through the cell membranes and accumulate into the cytoplasm both when administered alone and with the adsorbed benzo(α)pyrene. Proteomics revealed that the effect of carbon nanopowder-benzo(α)pyrene complex seems to be related to a new toxicological behavior instead of simple additive or synergistic effects. In detail, the cellular pathways modulated by the complex were mainly related to energy shift (glycolysis and pentose phosphate pathway), apoptosis, stress response and cellular trafficking.
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Affiliation(s)
- A Binelli
- Department of Biosciences, University of Milan, Italy.
| | - S Magni
- Department of Biosciences, University of Milan, Italy.
| | - C La Porta
- Department of Environmental Science and Policy, University of Milan, Italy; Center for Complexity & Biosystem, University of Milan, Italy
| | - L Bini
- Department of Life Science, University of Siena, Italy
| | - C Della Torre
- Department of Biosciences, University of Milan, Italy
| | - M Ascagni
- Department of Biosciences, University of Milan, Italy; UNITECH-NOLIMITS Platform, University of Milan, Italy
| | - D Maggioni
- Department of Chemistry, University of Milan, Italy
| | - A Ghilardi
- Department of Biosciences, University of Milan, Italy
| | - A Armini
- Department of Life Science, University of Siena, Italy
| | - C Landi
- Department of Life Science, University of Siena, Italy
| | - N Santo
- Department of Biosciences, University of Milan, Italy; UNITECH-NOLIMITS Platform, University of Milan, Italy
| | - L Madaschi
- Department of Biosciences, University of Milan, Italy; UNITECH-NOLIMITS Platform, University of Milan, Italy
| | - V Coccè
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Italy
| | - F Mutti
- Department of Environmental Science and Policy, University of Milan, Italy; Center for Complexity & Biosystem, University of Milan, Italy
| | - M C Lionetti
- Department of Environmental Science and Policy, University of Milan, Italy; Center for Complexity & Biosystem, University of Milan, Italy
| | - E Ciusani
- Department of Diagnostics and Applied Technology, Istituto Neurologico Carlo Besta, Milan, Italy
| | - L Del Giacco
- Department of Biosciences, University of Milan, Italy
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Ontañon OM, Landi C, Carleo A, Gagliardi A, Bianchi L, González PS, Agostini E, Bini L. What makes A. guillouiae SFC 500-1A able to co-metabolize phenol and Cr(VI)? A proteomic approach. J Hazard Mater 2018; 354:215-224. [PMID: 29753190 DOI: 10.1016/j.jhazmat.2018.04.068] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 04/24/2018] [Accepted: 04/25/2018] [Indexed: 06/08/2023]
Abstract
Acinetobacter guillouiae SFC 500-1A is an environmental bacterium able to efficiently co-remediate phenol and Cr(VI). To further understand the molecular mechanisms triggered in this strain during the bioremediation process, variations in the proteomic profile after treatment with phenol and phenol plus Cr(VI) were evaluated. The proteomic analysis revealed the induction of the β-ketoadipate pathway for phenol oxidation and the assimilation of degradation products through TCA cycle and glyoxylate shunt. Phenol exposure increased the abundance of proteins associated to energetic processes and ATP synthesis, but it also triggered cellular stress. The lipid bilayer was suggested as a target of phenol toxicity, and changing fatty acids composition seemed to be the bacterial response to protect the membrane integrity. The involvement of two flavoproteins in Cr(VI) reduction to Cr(III) was also proposed. The results suggested the important role of chaperones, antioxidant response and SOS-induced proteins in the ability of the strain to mitigate the damage generated by phenol and Cr(VI). This research contributes to elucidate the mechanisms involved in A. guillouiae SFC 500-1A tolerance and co-remediation of phenol and Cr(VI). Such information may result useful not only to improve its bioremediation efficiency but also to identify putative markers of resistance in environmental bacteria.
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Affiliation(s)
- Ornella Mailén Ontañon
- Department of Molecular Biology, National University of Rio Cuarto, Córdoba, Argentina; National Council for Scientific and Technological Research (CONICET), Argentina.
| | - Claudia Landi
- Laboratory of Functional Proteomics, Department of Life Sciences, University of Siena, Siena, Italy
| | - Alfonso Carleo
- Laboratory of Functional Proteomics, Department of Life Sciences, University of Siena, Siena, Italy; Current address: Department of Pulmonology, Hannover Medical School, Hannover, Germany
| | - Assunta Gagliardi
- Laboratory of Functional Proteomics, Department of Life Sciences, University of Siena, Siena, Italy; Current address: Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Laura Bianchi
- Laboratory of Functional Proteomics, Department of Life Sciences, University of Siena, Siena, Italy
| | - Paola Solange González
- Department of Molecular Biology, National University of Rio Cuarto, Córdoba, Argentina; National Council for Scientific and Technological Research (CONICET), Argentina
| | - Elizabeth Agostini
- Department of Molecular Biology, National University of Rio Cuarto, Córdoba, Argentina; National Council for Scientific and Technological Research (CONICET), Argentina
| | - Luca Bini
- Laboratory of Functional Proteomics, Department of Life Sciences, University of Siena, Siena, Italy
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Bianchi L, Carnemolla C, Viviani V, Landi C, Pavone V, Luddi A, Piomboni P, Bini L. Soluble protein fraction of human seminal plasma. J Proteomics 2018; 174:85-100. [DOI: 10.1016/j.jprot.2017.12.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 12/04/2017] [Accepted: 12/21/2017] [Indexed: 12/28/2022]
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Puglia M, Landi C, Gagliardi A, Breslin L, Armini A, Brunetti J, Pini A, Bianchi L, Bini L. The proteome speciation of an immortalized cystic fibrosis cell line: New perspectives on the pathophysiology of the disease. J Proteomics 2018; 170:28-42. [DOI: 10.1016/j.jprot.2017.09.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/01/2017] [Accepted: 09/25/2017] [Indexed: 01/04/2023]
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Parolini M, Bini L, Magni S, Rizzo A, Ghilardi A, Landi C, Armini A, Del Giacco L, Binelli A. Exposure to cocaine and its main metabolites altered the protein profile of zebrafish embryos. Environ Pollut 2018; 232:603-614. [PMID: 28993024 DOI: 10.1016/j.envpol.2017.09.097] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 09/13/2017] [Accepted: 09/28/2017] [Indexed: 06/07/2023]
Abstract
Illicit drugs have been identified as emerging aquatic pollutants because of their widespread presence in freshwaters and potential toxicity towards aquatic organisms. Among illicit drug residues, cocaine (COC) and its main metabolites, namely benzoylecgonine (BE) and ecgonine methyl ester (EME), are commonly detected in freshwaters worldwide at concentration that can induce diverse adverse effects to non-target organisms. However, the information of toxicity and mechanisms of action (MoA) of these drugs, mainly of COC metabolites, to aquatic species is still fragmentary and inadequate. Thus, this study was aimed at investigating the toxicity of two concentrations (0.3 and 1.0 μg/L) of COC, BE and EME similar to those found in aquatic ecosystems on zebrafish (Danio rerio) embryos at 96 h post fertilization through a functional proteomics approach. Exposure to COC and both its metabolites significantly altered the protein profile of zebrafish embryos, modulating the expression of diverse proteins belonging to different functional classes, including cytoskeleton, eye constituents, lipid transport, lipid and energy metabolism, and stress response. Expression of vitellogenins and crystallins was modulated by COC and both its main metabolites, while only BE and EME altered proteins related to lipid and energy metabolism, as well as to oxidative stress response. Our data confirmed the potential toxicity of low concentrations of COC, BE and EME, and helped to shed light on their MoA on an aquatic vertebrate during early developmental period.
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Affiliation(s)
- Marco Parolini
- Department of Environmental Science and Policy, University of Milan, via Celoria 2, I-20133 Milano, Italy.
| | - Luca Bini
- Department of Life Sciences, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Stefano Magni
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Alessandro Rizzo
- Department of Environmental Science and Policy, University of Milan, via Celoria 2, I-20133 Milano, Italy
| | - Anna Ghilardi
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Claudia Landi
- Department of Life Sciences, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Alessandro Armini
- Department of Life Sciences, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Luca Del Giacco
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Andrea Binelli
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
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Onelli E, Moscatelli A, Gagliardi A, Zaninelli M, Bini L, Baldi A, Caccianiga M, Reggi S, Rossi L. Retarded germination of Nicotiana tabacum seeds following insertion of exogenous DNA mimics the seed persistent behavior. PLoS One 2017; 12:e0187929. [PMID: 29216220 PMCID: PMC5720674 DOI: 10.1371/journal.pone.0187929] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 11/09/2017] [Indexed: 01/23/2023] Open
Abstract
Tobacco seeds show a coat-imposed dormancy in which the seed envelope tissues (testa and endosperm) impose a physical constraint on the radicle protrusion. The germination-limiting process is represented by the endosperm rupture which is induced by cell-wall weakening. Transgenic tobacco seeds, obtained by insertion of exogenous genes codifying for seed-based oral vaccines (F18 and VT2eB), showed retarded germination with respect to the wild type and modified the expression of endogenous proteins. Morphological and proteomic analyses of wild type and transgenic seeds revealed new insights into factors influencing seed germination. Our data showed that the interference of exogenous DNA influences the germination rather than the dormancy release, by modifying the maturation process. Dry seeds of F18 and VT2eB transgenic lines accumulated a higher amount of reserve and stress-related proteins with respect to the wild type. Moreover, the storage proteins accumulated in tobacco F18 and VT2eB dry seeds have structural properties that do not enable the early limited proteolysis observed in the wild type. Morphological observations by electron and light microscopy revealed a retarded mobilization of the storage material from protein and lipid bodies in transgenic seeds, thus impairing water imbibition and embryo elongation. In addition, both F18 and VT2eB dry seeds are more rounded than the wild type. Both the morphological and biochemical characteristics of transgenic seeds mimic the seed persistent profile, in which their roundness enables them to be buried in the soil, while the higher content of storage material enables the hypocotyl to elongate more and the cotyledons to emerge.
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Affiliation(s)
| | | | - Assunta Gagliardi
- Laboratory of Functional Proteomic, Department of Life Science, University of Siena, Siena, Italy
| | - Mauro Zaninelli
- Department of Human Sciences and Quality of Life Promotion, Università Telematica San Raffaele Roma, Italy, Rome, Italy
| | - Luca Bini
- Laboratory of Functional Proteomic, Department of Life Science, University of Siena, Siena, Italy
| | - Antonella Baldi
- Department of Health, Animal Science and Food Safety, Università degli Studi di Milano, Milan, Italy
| | | | | | - Luciana Rossi
- Department of Health, Animal Science and Food Safety, Università degli Studi di Milano, Milan, Italy
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D'Anna C, Cigna D, Di Sano C, Di Vincenzo S, Dino P, Ferraro M, Bini L, Bianchi L, Di Gaudio F, Gjomarkaj M, Pace E. Exposure to cigarette smoke extract and lipopolysaccharide modifies cytoskeleton organization in bronchial epithelial cells. Exp Lung Res 2017; 43:347-358. [PMID: 29199880 DOI: 10.1080/01902148.2017.1377784] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The integrity of the respiratory epithelium is crucial for airway homeostasis. Tobacco smoke exposure and recurrent infections of the airways play a crucial role in the progression and in the decline of the respiratory function in chronic obstructive pulmonary disease (COPD). The aim of this study was to detect differentially expressed proteins in a bronchial epithelial cell line (16-HBE) stimulated with cigarette smoke extract (CSE) and lipopolysaccharide (LPS), a constituent of gram-negative bacteria, alone and/or in combination, by using two-dimensional electrophoresis (2DE) analysis coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Western blot analysis was applied to confirm the expression of significantly modulated proteins. Flow cytometry and immunofluorescence were used to assess F-actin polimerization by phalloidin method. Fourteen proteins, with significant (p < 0.05) changes in intensity, were identified at various experimental points: 6 were up-regulated and 8 were down-regulated. As expected, bioinformatic analysis revealed that most of these proteins are involved in anti-oxidant and immune responses and in cytoskeleton stability. Western blot analysis confirmed that: Proteasome activator complex subunit 2 (PSME2), Peroxiredoxin-6 (PRDX6), Annexin A5 (ANXA5) and Heat shock protein beta-1 (HSPB1) were reduced and Coactosin-like protein (COTL-1) was increased by co-exposure of CSE and LPS. Furthermore, LPS and CSE increased actin polimerization. In conclusion, although further validation studies are needed, our findings suggest that, CSE and LPS could contribute to the progressive deterioration of lung function, altering the expression of proteins involved in metabolic processes and cytoskeleton rearrangement in bronchial epithelial cells.
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Affiliation(s)
- Claudia D'Anna
- a Department of Biomedicine , Institute of Biomedicine and Molecular Immunology (IBIM), CNR , Palermo , Italy
| | - Diego Cigna
- a Department of Biomedicine , Institute of Biomedicine and Molecular Immunology (IBIM), CNR , Palermo , Italy
| | - Caterina Di Sano
- a Department of Biomedicine , Institute of Biomedicine and Molecular Immunology (IBIM), CNR , Palermo , Italy
| | - Serena Di Vincenzo
- a Department of Biomedicine , Institute of Biomedicine and Molecular Immunology (IBIM), CNR , Palermo , Italy
| | - Paola Dino
- a Department of Biomedicine , Institute of Biomedicine and Molecular Immunology (IBIM), CNR , Palermo , Italy
| | - Maria Ferraro
- a Department of Biomedicine , Institute of Biomedicine and Molecular Immunology (IBIM), CNR , Palermo , Italy
| | - Luca Bini
- b Molecular Biology Department , Laboratory of Functional Proteomics, Università degli Studi di Siena , Siena , Italy
| | - Laura Bianchi
- b Molecular Biology Department , Laboratory of Functional Proteomics, Università degli Studi di Siena , Siena , Italy
| | - Francesca Di Gaudio
- c DiBiMeF (Biopatologia e Biotecnologie Mediche e Forensi) - Università degli Studi di Palermo - Italy
| | - Mark Gjomarkaj
- a Department of Biomedicine , Institute of Biomedicine and Molecular Immunology (IBIM), CNR , Palermo , Italy
| | - Elisabetta Pace
- a Department of Biomedicine , Institute of Biomedicine and Molecular Immunology (IBIM), CNR , Palermo , Italy
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Gagliardi A, Besio R, Carnemolla C, Landi C, Armini A, Aglan M, Otaify G, Temtamy SA, Forlino A, Bini L, Bianchi L. Cytoskeleton and nuclear lamina affection in recessive osteogenesis imperfecta: A functional proteomics perspective. J Proteomics 2017; 167:46-59. [PMID: 28802583 PMCID: PMC5584732 DOI: 10.1016/j.jprot.2017.08.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 08/02/2017] [Accepted: 08/07/2017] [Indexed: 02/07/2023]
Abstract
Osteogenesis imperfecta (OI) is a collagen-related disorder associated to dominant, recessive or X-linked transmission, mainly caused by mutations in type I collagen genes or in genes involved in type I collagen metabolism. Among the recessive forms, OI types VII, VIII, and IX are due to mutations in CRTAP, P3H1, and PPIB genes, respectively. They code for the three components of the endoplasmic reticulum complex that catalyzes 3-hydroxylation of type I collagen α1Pro986. Under-hydroxylation of this residue leads to collagen structural abnormalities and results in moderate to lethal OI phenotype, despite the exact molecular mechanisms are still not completely clear. To shed light on these recessive forms, primary fibroblasts from OI patients with mutations in CRTAP (n=3), P3H1 (n=3), PPIB (n=1) genes and from controls (n=4) were investigated by a functional proteomic approach. Cytoskeleton and nucleoskeleton asset, protein fate, and metabolism were delineated as mainly affected. While western blot experiments confirmed altered expression of lamin A/C and cofilin-1, immunofluorescence analysis using antibody against lamin A/C and phalloidin showed an aberrant organization of nucleus and cytoskeleton. This is the first report describing an altered organization of intracellular structural proteins in recessive OI and pointing them as possible novel target for OI treatment. SIGNIFICANCE OI is a prototype for skeletal dysplasias. It is a highly heterogeneous collagen-related disorder with dominant, recessive and X-linked transmission. There is no definitive cure for this disease, thus a better understanding of the molecular basis of its pathophysiology is expected to contribute in identifying potential targets to develop new treatments. Based on this concept, we performed a functional proteomic study to delineate affected molecular pathways in primary fibroblasts from recessive OI patients, carrying mutations in CRTAP (OI type VII), P3H1 (OI type VIII), and PPIB (OI type IX) genes. Our analyses demonstrated the occurrence of an altered cytoskeleton and, for the first time in OI, of nuclear lamina organization. Hence, cytoskeleton and nucleoskeleton components may be considered as novel drug targets for clinical management of the disease. Finally, according to our analyses, OI emerged to share similar deregulated pathways and molecular aberrances, as previously described, with other rare disorders caused by different genetic defects. Those aberrances may provide common pharmacological targets to support classical clinical approach in treating different diseases.
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Affiliation(s)
- Assunta Gagliardi
- Functional Proteomics Laboratory, Department of Life Sciences, University of Siena, Siena, Italy; CIBIO, University of Trento, Trento, Italy
| | - Roberta Besio
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - Chiara Carnemolla
- Functional Proteomics Laboratory, Department of Life Sciences, University of Siena, Siena, Italy
| | - Claudia Landi
- Functional Proteomics Laboratory, Department of Life Sciences, University of Siena, Siena, Italy
| | - Alessandro Armini
- Functional Proteomics Laboratory, Department of Life Sciences, University of Siena, Siena, Italy
| | - Mona Aglan
- Department of Clinical Genetics, Human Genetics & Genome Research Division, Center of Excellence for Human Genetics, National Research Centre, Cairo, Egypt
| | - Ghada Otaify
- Department of Clinical Genetics, Human Genetics & Genome Research Division, Center of Excellence for Human Genetics, National Research Centre, Cairo, Egypt
| | - Samia A Temtamy
- Department of Clinical Genetics, Human Genetics & Genome Research Division, Center of Excellence for Human Genetics, National Research Centre, Cairo, Egypt
| | - Antonella Forlino
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - Luca Bini
- Functional Proteomics Laboratory, Department of Life Sciences, University of Siena, Siena, Italy
| | - Laura Bianchi
- Functional Proteomics Laboratory, Department of Life Sciences, University of Siena, Siena, Italy.
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Fantappiè L, Irene C, De Santis M, Armini A, Gagliardi A, Tomasi M, Parri M, Cafardi V, Bonomi S, Ganfini L, Zerbini F, Zanella I, Carnemolla C, Bini L, Grandi A, Grandi G. Some Gram-negative Lipoproteins Keep Their Surface Topology When Transplanted from One Species to Another and Deliver Foreign Polypeptides to the Bacterial Surface. Mol Cell Proteomics 2017; 16:1348-1364. [PMID: 28483926 PMCID: PMC5500766 DOI: 10.1074/mcp.m116.065094] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 05/05/2017] [Indexed: 11/29/2022] Open
Abstract
In Gram-negative bacteria, outer membrane-associated lipoproteins can either face the periplasm or protrude out of the bacterial surface. The mechanisms involved in lipoprotein transport through the outer membrane are not fully elucidated. Some lipoproteins reach the surface by using species-specific transport machinery. By contrast, a still poorly characterized group of lipoproteins appears to always cross the outer membrane, even when transplanted from one organism to another. To investigate such lipoproteins, we tested the expression and compartmentalization in E. coli of three surface-exposed lipoproteins, two from Neisseria meningitidis (Nm-fHbp and NHBA) and one from Aggregatibacter actinomycetemcomitans (Aa-fHbp). We found that all three lipoproteins were lipidated and compartmentalized in the E. coli outer membrane and in outer membrane vesicles. Furthermore, fluorescent antibody cell sorting analysis, proteolytic surface shaving, and confocal microscopy revealed that all three proteins were also exposed on the surface of the outer membrane. Removal or substitution of the first four amino acids following the lipidated cysteine residue and extensive deletions of the C-terminal regions in Nm-fHbp did not prevent the protein from reaching the surface of the outer membrane. Heterologous polypeptides, fused to the C termini of Nm-fHbp and NHBA, were efficiently transported to the E. coli cell surface and compartmentalized in outer membrane vesicles, demonstrating that these lipoproteins can be exploited in biotechnological applications requiring Gram-negative bacterial surface display of foreign polypeptides.
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Affiliation(s)
- Laura Fantappiè
- From the ‡Synthetic and Structural Vaccinology Unit, CIBIO, University of Trento, Via Sommarive, 9, 38123 Povo, Trento, Italy
| | - Carmela Irene
- From the ‡Synthetic and Structural Vaccinology Unit, CIBIO, University of Trento, Via Sommarive, 9, 38123 Povo, Trento, Italy
| | - Micaela De Santis
- From the ‡Synthetic and Structural Vaccinology Unit, CIBIO, University of Trento, Via Sommarive, 9, 38123 Povo, Trento, Italy
| | - Alessandro Armini
- §Functional Proteomics Lab., Department of Life Sciences, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Assunta Gagliardi
- §Functional Proteomics Lab., Department of Life Sciences, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Michele Tomasi
- From the ‡Synthetic and Structural Vaccinology Unit, CIBIO, University of Trento, Via Sommarive, 9, 38123 Povo, Trento, Italy
| | - Matteo Parri
- ¶Toscana Life Sciences Scientific Park, Via Fiorentina, 1 53100, Siena, Italy
| | - Valeria Cafardi
- From the ‡Synthetic and Structural Vaccinology Unit, CIBIO, University of Trento, Via Sommarive, 9, 38123 Povo, Trento, Italy
| | - Serena Bonomi
- From the ‡Synthetic and Structural Vaccinology Unit, CIBIO, University of Trento, Via Sommarive, 9, 38123 Povo, Trento, Italy
| | - Luisa Ganfini
- From the ‡Synthetic and Structural Vaccinology Unit, CIBIO, University of Trento, Via Sommarive, 9, 38123 Povo, Trento, Italy
| | - Francesca Zerbini
- From the ‡Synthetic and Structural Vaccinology Unit, CIBIO, University of Trento, Via Sommarive, 9, 38123 Povo, Trento, Italy
| | - Ilaria Zanella
- From the ‡Synthetic and Structural Vaccinology Unit, CIBIO, University of Trento, Via Sommarive, 9, 38123 Povo, Trento, Italy
| | - Chiara Carnemolla
- §Functional Proteomics Lab., Department of Life Sciences, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Luca Bini
- §Functional Proteomics Lab., Department of Life Sciences, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Alberto Grandi
- ¶Toscana Life Sciences Scientific Park, Via Fiorentina, 1 53100, Siena, Italy
| | - Guido Grandi
- From the ‡Synthetic and Structural Vaccinology Unit, CIBIO, University of Trento, Via Sommarive, 9, 38123 Povo, Trento, Italy;
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Munzi S, Sheppard LJ, Leith ID, Cruz C, Branquinho C, Bini L, Gagliardi A, Cai G, Parrotta L. The cost of surviving nitrogen excess: energy and protein demand in the lichen Cladonia portentosa as revealed by proteomic analysis. Planta 2017; 245:819-833. [PMID: 28054148 DOI: 10.1007/s00425-017-2647-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 01/01/2017] [Indexed: 05/10/2023]
Abstract
Different nitrogen forms affect different metabolic pathways in lichens. In particular, the most relevant changes in protein expression were observed in the fungal partner, with NO 3- mostly affecting the energetic metabolism and NH 4+ affecting transport and regulation of proteins and the energetic metabolism much more than NO 3- did. Excess deposition of reactive nitrogen is a well-known agent of stress for lichens, but which symbiont is most affected and how, remains a mystery. Using proteomics can expand our understanding of stress effects on lichens. We investigated the effects of different doses and forms of reactive nitrogen, with and without supplementary phosphorus and potassium, on the proteome of the lichen Cladonia portentosa growing in a 'real-world' simulation of nitrogen deposition. Protein expression changed with the nitrogen treatments but mostly in the fungal partner, with NO3- mainly affecting the energetic metabolism and NH4+ also affecting the protein synthesis machinery. The photobiont mainly responded overexpressing proteins involved in energy production. This suggests that in response to nitrogen stress, the photobiont mainly supports the defensive mechanisms initiated by the mycobiont with an increased energy production. Such surplus energy is then used by the cell to maintain functionality in the presence of NO3-, while a futile cycle of protein production can be hypothesized to be induced by NH4+ excess. External supply of potassium and phosphorus influenced differently the responses of particular enzymes, likely reflecting the many processes in which potassium exerts a regulatory function.
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Affiliation(s)
- Silvana Munzi
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Bloco C2, 1749-016, Lisbon, Portugal.
| | - Lucy J Sheppard
- Centre for Ecology and Hydrology (CEH) Edinburgh, Bush Estate, Penicuik, EH26 0QB, UK
| | - Ian D Leith
- Centre for Ecology and Hydrology (CEH) Edinburgh, Bush Estate, Penicuik, EH26 0QB, UK
| | - Cristina Cruz
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Bloco C2, 1749-016, Lisbon, Portugal
| | - Cristina Branquinho
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Bloco C2, 1749-016, Lisbon, Portugal
| | - Luca Bini
- Department of Life Sciences, University of Siena, Via Aldo Moro, 2, 53100, Siena, Italy
| | - Assunta Gagliardi
- Department of Life Sciences, University of Siena, Via Aldo Moro, 2, 53100, Siena, Italy
| | - Giampiero Cai
- Department of Life Sciences, University of Siena, Via Pier Andrea Mattioli, 4, 53100, Siena, Italy
| | - Luigi Parrotta
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Irnerio, 42, 40126, Bologna, Italy
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Binelli A, Del Giacco L, Santo N, Bini L, Magni S, Parolini M, Madaschi L, Ghilardi A, Maggioni D, Ascagni M, Armini A, Prosperi L, Landi C, La Porta C, Della Torre C. Carbon nanopowder acts as a Trojan-horse for benzo(α)pyrene in Danio rerio embryos. Nanotoxicology 2017; 11:371-381. [DOI: 10.1080/17435390.2017.1306130] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- A. Binelli
- Department of Biosciences, University of Milan, Milan, Italy
| | - L. Del Giacco
- Department of Biosciences, University of Milan, Milan, Italy
| | - N. Santo
- Department of Biosciences, University of Milan, Milan, Italy
| | - L. Bini
- Department of Life Science, University of Siena, Siena, Italy
| | - S. Magni
- Department of Biosciences, University of Milan, Milan, Italy
| | - M. Parolini
- Department of Biosciences, University of Milan, Milan, Italy
| | - L. Madaschi
- Department of Biosciences, University of Milan, Milan, Italy
| | - A. Ghilardi
- Department of Biosciences, University of Milan, Milan, Italy
| | - D. Maggioni
- Department of Chemistry, University of Milan, Milan, Italy
| | - M. Ascagni
- Department of Biosciences, University of Milan, Milan, Italy
| | - A. Armini
- Department of Life Science, University of Siena, Siena, Italy
| | - L. Prosperi
- Department of Biosciences, University of Milan, Milan, Italy
| | - C. Landi
- Department of Life Science, University of Siena, Siena, Italy
| | - C. La Porta
- Department of Biosciences, University of Milan, Milan, Italy
| | - C. Della Torre
- Department of Biosciences, University of Milan, Milan, Italy
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40
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Cortelazzo A, de Felice C, Leoncini S, Signorini C, Guerranti R, Leoncini R, Armini A, Bini L, Ciccoli L, Hayek J. Inflammatory protein response in CDKL5-Rett syndrome: evidence of a subclinical smouldering inflammation. Inflamm Res 2016; 66:269-280. [PMID: 27900411 DOI: 10.1007/s00011-016-1014-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 11/06/2016] [Accepted: 11/23/2016] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Mutations in the cyclin-dependent kinase-like 5 gene cause a clinical variant of Rett syndrome (CDKL5-RTT). A role for the acute-phase response (APR) is emerging in typical RTT caused by methyl-CpG-binding protein 2 gene mutations (MECP2-RTT). No information is, to date, available on the inflammatory protein response in CDKL5-RTT. We evaluated, for the first time, the APR protein response in CDKL5-RTT. METHODS Protein patterns in albumin- and IgG-depleted plasma proteome from CDKL5-RTT patients were evaluated by two-dimensional gel electrophoresis/mass spectrometry. The resulting data were related to circulating cytokines and compared to healthy controls or MECP2-RTT patients. The effects of omega-3 polyunsaturated fatty acids (ω-3 PUFAs) were evaluated. RESULTS CDKL5-RTT mutations resulted in a subclinical attenuated inflammation, specifically characterized by an overexpression of the complement component C3 and CD5 antigen-like, both strictly related to the inflammatory response. Cytokine dysregulation featuring a bulk increase of anti-inflammatory cytokines, predominantly IL-10, could explain the unchanged erythrocyte sedimentation rate and atypical features of inflammation in CDKL5-RTT. Omega-3 PUFAs were able to counterbalance the pro-inflammatory status. CONCLUSION For the first time, we revealed a subclinical smouldering inflammation pattern in CDKL5-RTT consisting in the coexistence of an atypical APR coupled with a dysregulated cytokine response.
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Affiliation(s)
- Alessio Cortelazzo
- Child Neuropsychiatry Unit, University Hospital Azienda Ospedaliera Universitaria Senese (AOUS), Viale M. Bracci 16, 53100, Siena, Italy. .,Department of Medical Biotechnologies, University of Siena, Via A. Moro 2, 53100, Siena, Italy. .,Clinical Pathology Laboratory Unit, University Hospital AOUS, Viale M. Bracci 16, 53100, Siena, Italy.
| | - Claudio de Felice
- Neonatal Intensive Care Unit, University Hospital AOUS, Viale M. Bracci 16, 53100, Siena, Italy
| | - Silvia Leoncini
- Child Neuropsychiatry Unit, University Hospital Azienda Ospedaliera Universitaria Senese (AOUS), Viale M. Bracci 16, 53100, Siena, Italy.,Department of Molecular and Developmental Medicine, University of Siena, Via A. Moro 6, 53100, Siena, Italy
| | - Cinzia Signorini
- Department of Molecular and Developmental Medicine, University of Siena, Via A. Moro 6, 53100, Siena, Italy
| | - Roberto Guerranti
- Department of Medical Biotechnologies, University of Siena, Via A. Moro 2, 53100, Siena, Italy.,Clinical Pathology Laboratory Unit, University Hospital AOUS, Viale M. Bracci 16, 53100, Siena, Italy
| | - Roberto Leoncini
- Department of Medical Biotechnologies, University of Siena, Via A. Moro 2, 53100, Siena, Italy.,Clinical Pathology Laboratory Unit, University Hospital AOUS, Viale M. Bracci 16, 53100, Siena, Italy
| | - Alessandro Armini
- Department of Life Sciences, University of Siena, Via A. Moro 2, 53100, Siena, Italy
| | - Luca Bini
- Department of Life Sciences, University of Siena, Via A. Moro 2, 53100, Siena, Italy
| | - Lucia Ciccoli
- Department of Molecular and Developmental Medicine, University of Siena, Via A. Moro 6, 53100, Siena, Italy
| | - Joussef Hayek
- Child Neuropsychiatry Unit, University Hospital Azienda Ospedaliera Universitaria Senese (AOUS), Viale M. Bracci 16, 53100, Siena, Italy
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Aloisi I, Parrotta L, Ruiz KB, Landi C, Bini L, Cai G, Biondi S, Del Duca S. New Insight into Quinoa Seed Quality under Salinity: Changes in Proteomic and Amino Acid Profiles, Phenolic Content, and Antioxidant Activity of Protein Extracts. Front Plant Sci 2016; 7:656. [PMID: 27242857 PMCID: PMC4870233 DOI: 10.3389/fpls.2016.00656] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 04/28/2016] [Indexed: 05/27/2023]
Abstract
Quinoa (Chenopodium quinoa Willd) is an ancient Andean seed-producing crop well known for its exceptional nutritional properties and resistance to adverse environmental conditions, such as salinity and drought. Seed storage proteins, amino acid composition, and bioactive compounds play a crucial role in determining the nutritional value of quinoa. Seeds harvested from three Chilean landraces of quinoa, one belonging to the salares ecotype (R49) and two to the coastal-lowlands ecotype, VI-1 and Villarrica (VR), exposed to two levels of salinity (100 and 300 mM NaCl) were used to conduct a sequential extraction of storage proteins in order to obtain fractions enriched in albumins/globulins, 11S globulin and in prolamin-like proteins. The composition of the resulting protein fractions was analyzed by one- and two-dimensional polyacrylamide gel electrophoresis. Results confirmed a high polymorphism in seed storage proteins; the two most representative genotype-specific bands of the albumin/globulin fraction were the 30- and 32-kDa bands, while the 11S globulin showed genotype-specific polymorphism for the 40- and 42-kDa bands. Spot analysis by mass spectrometry followed by in silico analyses were conducted to identify the proteins whose expression changed most significantly in response to salinity in VR. Proteins belonging to several functional categories (i.e., stress protein, metabolism, and storage) were affected by salinity. Other nutritional and functional properties, namely amino acid profiles, total polyphenol (TPC) and flavonoid (TFC) contents, and antioxidant activity (AA) of protein extracts were also analyzed. With the exception of Ala and Met in R49, all amino acids derived from protein hydrolysis were diminished in seeds from salt-treated plants, especially in landrace VI-1. By contrast, several free amino acids were unchanged or increased by salinity in R49 as compared with VR and VI-1, suggesting a greater tolerance in the salares landrace. VR had the highest TPC and AA under non-saline conditions. Salinity increased TPC in all three landraces, with the strongest increase occurring in R49, and enhanced radical scavenging capacity in R49 and VR. Overall, results show that salinity deeply altered the seed proteome and amino acid profiles and, in general, increased the concentration of bioactive molecules and AA of protein extracts in a genotype-dependent manner.
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Affiliation(s)
- Iris Aloisi
- Department of Biological, Geological and Environmental Sciences, University of BolognaBologna, Italy
| | - Luigi Parrotta
- Department of Biological, Geological and Environmental Sciences, University of BolognaBologna, Italy
| | - Karina B. Ruiz
- Department of Biological, Geological and Environmental Sciences, University of BolognaBologna, Italy
- Departamento de Producción Agrícola, Universidad de ChileSantiago, Chile
| | - Claudia Landi
- Department of Life Sciences, University of SienaSiena, Italy
| | - Luca Bini
- Department of Life Sciences, University of SienaSiena, Italy
| | - Giampiero Cai
- Department of Life Sciences, University of SienaSiena, Italy
| | - Stefania Biondi
- Department of Biological, Geological and Environmental Sciences, University of BolognaBologna, Italy
| | - Stefano Del Duca
- Department of Biological, Geological and Environmental Sciences, University of BolognaBologna, Italy
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Carleo A, Bargagli E, Landi C, Bennett D, Bianchi L, Gagliardi A, Carnemolla C, Perari MG, Cillis G, Armini A, Bini L, Rottoli P. Comparative proteomic analysis of bronchoalveolar lavage of familial and sporadic cases of idiopathic pulmonary fibrosis. J Breath Res 2016; 10:026007. [DOI: 10.1088/1752-7155/10/2/026007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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43
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Gagliardi A, Lamboglia E, Bianchi L, Landi C, Armini A, Ciolfi S, Bini L, Marri L. Proteomics analysis of a long-term survival strain of Escherichia coli K-12 exhibiting a growth advantage in stationary-phase (GASP) phenotype. Proteomics 2016; 16:963-72. [PMID: 26711811 DOI: 10.1002/pmic.201500314] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 11/24/2015] [Accepted: 12/23/2015] [Indexed: 01/14/2023]
Abstract
The aim of this work was the functional and proteomic analysis of a mutant, W3110 Bgl(+) /10, isolated from a batch culture of an Escherichia coli K-12 strain maintained at room temperature without addition of nutrients for 10 years. When the mutant was evaluated in competition experiments in co-culture with the wild-type, it exhibited the growth advantage in stationary phase (GASP) phenotype. Proteomes of the GASP mutant and its parental strain were compared by using a 2DE coupled with MS approach. Several differentially expressed proteins were detected and many of them were successful identified by mass spectrometry. Identified expression-changing proteins were grouped into three functional categories: metabolism, protein synthesis, chaperone and stress responsive proteins. Among them, the prevalence was ascribable to the "metabolism" group (72%) for the GASP mutant, and to "chaperones and stress responsive proteins" group for the parental strain (48%).
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Affiliation(s)
| | | | - Laura Bianchi
- Department of Life Sciences, University of Siena, Siena, Italy
| | - Claudia Landi
- Department of Life Sciences, University of Siena, Siena, Italy
| | | | - Silvia Ciolfi
- Department of Life Sciences, University of Siena, Siena, Italy
| | - Luca Bini
- Department of Life Sciences, University of Siena, Siena, Italy
| | - Laura Marri
- Department of Life Sciences, University of Siena, Siena, Italy
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44
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Gamberi T, Magherini F, Fiaschi T, Landini I, Massai L, Valocchia E, Bianchi L, Bini L, Gabbiani C, Nobili S, Mini E, Messori L, Modesti A. Proteomic analysis of the cytotoxic effects induced by the organogold(III) complex Aubipyc in cisplatin-resistant A2780 ovarian cancer cells: further evidence for the glycolytic pathway implication. Mol Biosyst 2016; 11:1653-67. [PMID: 25906354 DOI: 10.1039/c5mb00008d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The cellular alterations produced in cisplatin-resistant A2780 ovarian cancer cells (A2780/R) upon treatment with the cytotoxic organogold(III) complex Aubipyc were investigated in depth through a classical proteomic approach. We observed that A2780/R cell exposure to a cytotoxic concentration of Aubipyc for 24 hours results in a conspicuous number of alterations at the protein level that were carefully examined. Notably, we observed that several affected proteins belong to the glucose metabolism system further supporting the idea that the cytotoxic effects of Aubipyc in A2780/R cells are mostly mediated by an impairment of glucose metabolism in excellent agreement with previous observations on the parent cisplatin-sensitive cell line.
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Affiliation(s)
- Tania Gamberi
- Department of Biomedical, Experimental and Clinical Sciences "Mario Serio", University of Florence, Viale Morgagni 50, Florence, Italy.
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Gistelinck C, Gioia R, Gagliardi A, Tonelli F, Marchese L, Bianchi L, Landi C, Bini L, Huysseune A, Witten PE, Staes A, Gevaert K, De Rocker N, Menten B, Malfait F, Leikin S, Carra S, Tenni R, Rossi A, De Paepe A, Coucke P, Willaert A, Forlino A. Zebrafish Collagen Type I: Molecular and Biochemical Characterization of the Major Structural Protein in Bone and Skin. Sci Rep 2016; 6:21540. [PMID: 26876635 PMCID: PMC4753508 DOI: 10.1038/srep21540] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 01/26/2016] [Indexed: 12/27/2022] Open
Abstract
Over the last years the zebrafish imposed itself as a powerful model to study skeletal diseases, but a limit to its use is the poor characterization of collagen type I, the most abundant protein in bone and skin. In tetrapods collagen type I is a trimer mainly composed of two α1 chains and one α2 chain, encoded by COL1A1 and COL1A2 genes, respectively. In contrast, in zebrafish three type I collagen genes exist, col1a1a, col1a1b and col1a2 coding for α1(I), α3(I) and α2(I) chains. During embryonic and larval development the three collagen type I genes showed a similar spatio-temporal expression pattern, indicating their co-regulation and interdependence at these stages. In both embryonic and adult tissues, the presence of the three α(I) chains was demonstrated, although in embryos α1(I) was present in two distinct glycosylated states, suggesting a developmental-specific collagen composition. Even though in adult bone, skin and scales equal amounts of α1(I), α3(I) and α2(I) chains are present, the presented data suggest a tissue-specific stoichiometry and/or post-translational modification status for collagen type I. In conclusion, this data will be useful to properly interpret results and insights gained from zebrafish models of skeletal diseases.
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Affiliation(s)
- C Gistelinck
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - R Gioia
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - A Gagliardi
- Functional Proteomics Lab., Department of Life Sciences, University of Siena, Siena, Italy
| | - F Tonelli
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - L Marchese
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - L Bianchi
- Functional Proteomics Lab., Department of Life Sciences, University of Siena, Siena, Italy
| | - C Landi
- Functional Proteomics Lab., Department of Life Sciences, University of Siena, Siena, Italy
| | - L Bini
- Functional Proteomics Lab., Department of Life Sciences, University of Siena, Siena, Italy
| | - A Huysseune
- Biology Department, Ghent University, Ghent, Belgium
| | - P E Witten
- Biology Department, Ghent University, Ghent, Belgium
| | - A Staes
- Department of Medical Protein Research, VIB, Ghent, Belgium.,Department of Biochemistry, Ghent University, Ghent, Belgium
| | - K Gevaert
- Department of Medical Protein Research, VIB, Ghent, Belgium.,Department of Biochemistry, Ghent University, Ghent, Belgium
| | - N De Rocker
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - B Menten
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - F Malfait
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - S Leikin
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - S Carra
- Department of Biosciences, University of Milano, Milan, Italy
| | - R Tenni
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - A Rossi
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - A De Paepe
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - P Coucke
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - A Willaert
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - A Forlino
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
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46
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Cortelazzo A, Felice C, Guerranti R, Leoncini R, Barducci A, Leoncini S, Signorini C, Zollo G, Pecorelli A, Gagliardi A, Armini A, Paccagnini E, Gentile M, Bini L, Durand T, Galano JM, Rossi M, Ciccoli L, Hayek J. Erythrocyte Cytoskeletal-plasma Membrane Protein Network in Rett Syndrome: Effects of .-3 Polyunsaturated Fatty Acids. CURR PROTEOMICS 2016. [DOI: 10.2174/157016461204160119153511] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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47
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Pietrovito L, Cano-Cortés V, Gamberi T, Magherini F, Bianchi L, Bini L, Sánchez-Martín RM, Fasano M, Modesti A. Cellular response to empty and palladium-conjugated amino-polystyrene nanospheres uptake: a proteomic study. Proteomics 2015; 15:34-43. [PMID: 25354928 DOI: 10.1002/pmic.201300423] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 09/30/2014] [Accepted: 10/23/2014] [Indexed: 11/08/2022]
Abstract
Amino polystyrene nanospheres are shown to be efficient and controllable delivery devices, capable of transporting several bioactive cargoes. Recently, the design of a new device for prodrug activation, using these nanospheres with palladium encapsulated onto them, has been developed successfully. To study the influence of the cellular uptake of these nanodevices, we investigated the cellular response of human embryonic kidney cells (HEK-293T) and murine fibroblasts (L929) treated with empty or palladium-conjugated amino polystyrene nanospheres. To identify differentially expressed proteins, we performed an exhaustive proteomic analysis. In accordance with genomic data previously obtained, the uptake of the empty nanospheres did not induce significant variation in protein expression levels. Following the treatment with palladium-conjugated nanospheres, some changes in protein profiles in both cell lines were observed; these alterations affect proteins involved in cell metabolism and intracellular transport. No key regulator of the cell cycle result was differentially expressed after the treatment, confirming that these innovative drug delivery systems are harmless and well tolerated by the cells.
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Affiliation(s)
- Laura Pietrovito
- Dipartimento di Scienze Biomediche, Sperimentali e Cliniche, Università degli Studi di Firenze, Italy
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Bianchi L, Gagliardi A, Maruelli S, Besio R, Landi C, Gioia R, Kozloff KM, Khoury BM, Coucke PJ, Symoens S, Marini JC, Rossi A, Bini L, Forlino A. Altered cytoskeletal organization characterized lethal but not surviving Brtl+/- mice: insight on phenotypic variability in osteogenesis imperfecta. Hum Mol Genet 2015; 24:6118-33. [PMID: 26264579 DOI: 10.1093/hmg/ddv328] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 08/06/2015] [Indexed: 02/02/2023] Open
Abstract
Osteogenesis imperfecta (OI) is a heritable bone disease with dominant and recessive transmission. It is characterized by a wide spectrum of clinical outcomes ranging from very mild to lethal in the perinatal period. The intra- and inter-familiar OI phenotypic variability in the presence of an identical molecular defect is still puzzling to the research field. We used the OI murine model Brtl(+/-) to investigate the molecular basis of OI phenotypic variability. Brtl(+/-) resembles classical dominant OI and shows either a moderately severe or a lethal outcome associated with the same Gly349Cys substitution in the α1 chain of type I collagen. A systems biology approach was used. We took advantage of proteomic pathway analysis to functionally link proteins differentially expressed in bone and skin of Brtl(+/-) mice with different outcomes to define possible phenotype modulators. The skin/bone and bone/skin hybrid networks highlighted three focal proteins: vimentin, stathmin and cofilin-1, belonging to or involved in cytoskeletal organization. Abnormal cytoskeleton was indeed demonstrated by immunohistochemistry to occur only in tissues from Brtl(+/-) lethal mice. The aberrant cytoskeleton affected osteoblast proliferation, collagen deposition, integrin and TGF-β signaling with impairment of bone structural properties. Finally, aberrant cytoskeletal assembly was detected in fibroblasts obtained from lethal, but not from non-lethal, OI patients carrying an identical glycine substitution. Our data demonstrated that compromised cytoskeletal assembly impaired both cell signaling and cellular trafficking in mutant lethal mice, altering bone properties. These results point to the cytoskeleton as a phenotypic modulator and potential novel target for OI treatment.
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Affiliation(s)
- Laura Bianchi
- Functional Proteomics Laboratory, Department of Life Sciences, University of Siena, Siena, Italy
| | - Assunta Gagliardi
- Functional Proteomics Laboratory, Department of Life Sciences, University of Siena, Siena, Italy
| | - Silvia Maruelli
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - Roberta Besio
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - Claudia Landi
- Functional Proteomics Laboratory, Department of Life Sciences, University of Siena, Siena, Italy
| | - Roberta Gioia
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - Kenneth M Kozloff
- Orthopaedic Research Laboratories, Department of Orthopaedic Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Basma M Khoury
- Orthopaedic Research Laboratories, Department of Orthopaedic Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Paul J Coucke
- Center for Medical Genetics, Ghent University, Ghent, Belgium and
| | - Sofie Symoens
- Center for Medical Genetics, Ghent University, Ghent, Belgium and
| | - Joan C Marini
- Bone and Extracellular Matrix Branch, NICHD, National Institute of Health, Bethesda, MD, USA
| | - Antonio Rossi
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - Luca Bini
- Functional Proteomics Laboratory, Department of Life Sciences, University of Siena, Siena, Italy
| | - Antonella Forlino
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy,
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Moscatelli A, Gagliardi A, Maneta-Peyret L, Bini L, Stroppa N, Onelli E, Landi C, Scali M, Idilli AI, Moreau P. Characterisation of detergent-insoluble membranes in pollen tubes of Nicotiana tabacum (L.). Biol Open 2015; 4:378-99. [PMID: 25701665 PMCID: PMC4359744 DOI: 10.1242/bio.201410249] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Pollen tubes are the vehicle for sperm cell delivery to the embryo sac during fertilisation of Angiosperms. They provide an intriguing model for unravelling mechanisms of growing to extremes. The asymmetric distribution of lipids and proteins in the pollen tube plasma membrane modulates ion fluxes and actin dynamics and is maintained by a delicate equilibrium between exocytosis and endocytosis. The structural constraints regulating polarised secretion and asymmetric protein distribution on the plasma membrane are mostly unknown. To address this problem, we investigated whether ordered membrane microdomains, namely membrane rafts, might contribute to sperm cell delivery. Detergent insoluble membranes, rich in sterols and sphingolipids, were isolated from tobacco pollen tubes. MALDI TOF/MS analysis revealed that actin, prohibitins and proteins involved in methylation reactions and in phosphoinositide pattern regulation are specifically present in pollen tube detergent insoluble membranes. Tubulins, voltage-dependent anion channels and proteins involved in membrane trafficking and signalling were also present. This paper reports the first evidence of membrane rafts in Angiosperm pollen tubes, opening new perspectives on the coordination of signal transduction, cytoskeleton dynamics and polarised secretion.
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Affiliation(s)
- Alessandra Moscatelli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Assunta Gagliardi
- Laboratorio di Proteomica Funzionale, Dipartimento di Scienze della Vita, Università degli Studi di Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Lilly Maneta-Peyret
- Laboratoire de Biogenèse Membranaire, Université Bordeaux Segalen, 71 Avenue Edouard Bourlaux, 33883 Villenave d'Ornon, France
| | - Luca Bini
- Laboratorio di Proteomica Funzionale, Dipartimento di Scienze della Vita, Università degli Studi di Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Nadia Stroppa
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Elisabetta Onelli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Claudia Landi
- Laboratorio di Proteomica Funzionale, Dipartimento di Scienze della Vita, Università degli Studi di Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Monica Scali
- Dipartimento di Scienze della Vita, Università degli Studi di Siena, Via P. A. Mattioli 4, 53100 Siena, Italy
| | - Aurora Irene Idilli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy Present address: Institute of Biophysics, National Research Council and FBK, 38123 Trento, Italy
| | - Patrick Moreau
- Laboratoire de Biogenèse Membranaire, Université Bordeaux Segalen, 71 Avenue Edouard Bourlaux, 33883 Villenave d'Ornon, France
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50
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Orlandini M, Galvagni F, Bardelli M, Rocchigiani M, Lentucci C, Anselmi F, Zippo A, Bini L, Oliviero S. The characterization of a novel monoclonal antibody against CD93 unveils a new antiangiogenic target. Oncotarget 2015; 5:2750-60. [PMID: 24809468 PMCID: PMC4058042 DOI: 10.18632/oncotarget.1887] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The inhibition of tumor angiogenesis is one of the main challenges in cancer therapy. With the aim of developing monoclonal antibodies able to inhibit angiogenesis, we immunized mice with proliferating human umbilical vein endothelial cells. We generated a library of monoclonal antibodies able to recognize antigens expressed on endothelial cells and screened the antibodies for their ability to inhibit endothelial cell proliferation, migration, and sprouting in vitro. Here, we show that the antibody, designated as 4E1, is able to neutralize the formation of new vessels both in vitro and in vivo without affecting endothelial cell survival. By mass spectrometry we identified CD93 as the antigen bound by 4E1 and mapped the recognized epitope. CD93 is a transmembrane protein heavily glycosylated preferentially expressed in the vascular endothelium. CD93 silencing by lentiviral-mediated small hairpin RNA expression impairs human endothelial cell proliferation, migration, and sprouting. Altogether these findings reveal 4E1 as a novel antiangiogenic antibody and identify CD93 as a new target suitable for antiangiogenic therapy.
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Affiliation(s)
- Maurizio Orlandini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro, 2 - 53100 Siena, Italy
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