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Carrozzini T, Pollaci G, Gorla G, Potenza A, Rifino N, Acerbi F, Vetrano IG, Ferroli P, Bersano A, Gianazza E, Banfi C, Gatti L. Proteome Profiling of the Dura Mater in Patients with Moyamoya Angiopathy. Int J Mol Sci 2023; 24:11194. [PMID: 37446373 DOI: 10.3390/ijms241311194] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 06/30/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023] Open
Abstract
Moyamoya angiopathy (MMA) is an uncommon cerebrovascular disease characterized by a progressive steno-occlusive lesion of the internal carotid artery and the compensatory development of an unstable network of collateral vessels. These vascular hallmarks are responsible for recurrent ischemic/hemorrhagic strokes. Surgical treatment represents the preferred procedure for MMA patients, and indirect revascularization may induce a spontaneous angiogenesis between the brain surface and dura mater (DM), whose function remains rather unknown. A better understanding of MMA pathogenesis is expected from the molecular characterization of DM. We performed a comprehensive, label-free, quantitative mass spectrometry-based proteomic characterization of DM. The 30 most abundant identified proteins were located in the extracellular region or exosomes and were involved in extracellular matrix organization. Gene ontology analysis revealed that most proteins were involved in binding functions and hydrolase activity. Among the 30 most abundant proteins, Filamin A is particularly relevant because considering its well-known biochemical functions and molecular features, it could be a possible second hit gene with a potential role in MMA pathogenesis. The current explorative study could pave the way for further analyses aimed at better understanding such uncommon and disabling intracranial vasculopathy.
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Affiliation(s)
- Tatiana Carrozzini
- Laboratory of Neurobiology and UCV, Neurology IX Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Giuliana Pollaci
- Laboratory of Neurobiology and UCV, Neurology IX Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
- Department of Pharmacological and Biomolecular Sciences, Università di Milano, 20133 Milan, Italy
| | - Gemma Gorla
- Laboratory of Neurobiology and UCV, Neurology IX Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Antonella Potenza
- Laboratory of Neurobiology and UCV, Neurology IX Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Nicola Rifino
- Laboratory of Neurobiology and UCV, Neurology IX Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Francesco Acerbi
- Department of Neurosurgery, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
- Experimental Microsurgical Laboratory, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Ignazio G Vetrano
- Department of Neurosurgery, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
- Department of Biomedical Sciences for Health, Università di Milano, 20133 Milan, Italy
| | - Paolo Ferroli
- Department of Neurosurgery, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Anna Bersano
- Laboratory of Neurobiology and UCV, Neurology IX Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Erica Gianazza
- Unit of Functional Proteomics, Metabolomics, and Network Analysis, Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy
| | - Cristina Banfi
- Unit of Functional Proteomics, Metabolomics, and Network Analysis, Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy
| | - Laura Gatti
- Laboratory of Neurobiology and UCV, Neurology IX Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
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Prenylcysteine Oxidase 1 Is a Key Regulator of Adipogenesis. Antioxidants (Basel) 2023; 12:antiox12030542. [PMID: 36978789 PMCID: PMC10045348 DOI: 10.3390/antiox12030542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/18/2023] [Accepted: 02/19/2023] [Indexed: 02/24/2023] Open
Abstract
The process of adipogenesis involves the differentiation of preadipocytes into mature adipocytes. Excessive adipogenesis promotes obesity, a condition that increasingly threatens global health and contributes to the rapid rise of obesity-related diseases. We have recently shown that prenylcysteine oxidase 1 (PCYOX1) is a regulator of atherosclerosis-disease mechanisms, which acts through mechanisms not exclusively related to its pro-oxidant activity. To address the role of PCYOX1 in the adipogenic process, we extended our previous observations confirming that Pcyox1−/−/Apoe−/− mice fed a high-fat diet for 8 or 12 weeks showed significantly lower body weight, when compared to Pcyox1+/+/Apoe−/− mice, due to an evident reduction in visceral adipose content. We herein assessed the role of PCYOX1 in adipogenesis. Here, we found that PCYOX1 is expressed in adipose tissue, and, independently from its pro-oxidant enzymatic activity, is critical for adipogenesis. Pcyox1 gene silencing completely prevented the differentiation of 3T3-L1 preadipocytes, by acting as an upstream regulator of several key players, such as FABP4, PPARγ, C/EBPα. Proteomic analysis, performed by quantitative label-free mass spectrometry, further strengthened the role of PCYOX1 in adipogenesis by expanding the list of its downstream targets. Finally, the absence of Pcyox1 reduces the inflammatory markers in adipose tissue. These findings render PCYOX1 a novel adipogenic factor with possible pathophysiological or therapeutic potential.
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3
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Greco MF, Rizzuto AS, Zarà M, Cafora M, Favero C, Solazzo G, Giusti I, Adorni MP, Zimetti F, Dolo V, Banfi C, Ferri N, Sirtori CR, Corsini A, Barbieri SS, Pistocchi A, Bollati V, Macchi C, Ruscica M. PCSK9 Confers Inflammatory Properties to Extracellular Vesicles Released by Vascular Smooth Muscle Cells. Int J Mol Sci 2022; 23:13065. [PMID: 36361853 PMCID: PMC9655172 DOI: 10.3390/ijms232113065] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 10/21/2022] [Accepted: 10/23/2022] [Indexed: 10/20/2023] Open
Abstract
Vascular smooth muscle cells (VSMCs) are key participants in both early- and late-stage atherosclerosis and influence neighbouring cells possibly by means of bioactive molecules, some of which are packed into extracellular vesicles (EVs). Proprotein convertase subtilisin/kexin type 9 (PCSK9) is expressed and secreted by VSMCs. This study aimed to unravel the role of PCSK9 on VSMCs-derived EVs in terms of content and functionality. EVs were isolated from human VSMCs overexpressing human PCSK9 (VSMCPCSK9-EVs) and tested on endothelial cells, monocytes, macrophages and in a model of zebrafish embryos. Compared to EVs released from wild-type VSMCs, VSMCPCSK9-EVs caused a rise in the expression of adhesion molecules in endothelial cells and of pro-inflammatory cytokines in monocytes. These acquired an increased migratory capacity, a reduced oxidative phosphorylation and secreted proteins involved in immune response and immune effector processes. Concerning macrophages, VSMCPCSK9-EVs enhanced inflammatory milieu and uptake of oxidized low-density lipoproteins, whereas the migratory capacity was reduced. When injected into zebrafish embryos, VSMCPCSK9-EVs favoured the recruitment of macrophages toward the site of injection. The results of the present study provide evidence that PCSK9 plays an inflammatory role by means of EVs, at least by those derived from smooth muscle cells of vascular origin.
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Affiliation(s)
- Maria Francesca Greco
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, 20133 Milan, Italy
| | - Alessandra Stefania Rizzuto
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, 20133 Milan, Italy
| | - Marta Zarà
- Centro Cardiologico Monzino, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), 20133 Milan, Italy
| | - Marco Cafora
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, 20133 Milan, Italy
| | - Chiara Favero
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, 20133 Milan, Italy
| | - Giulia Solazzo
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, 20133 Milan, Italy
| | - Ilaria Giusti
- Department of Life, Health and Environmental Sciences, Università degli Studi dell'Aquila, 67100 L'Aquila, Italy
| | - Maria Pia Adorni
- Unit of Neuroscience, Department of Medicine and Surgery, Università degli Studi di Parma, 43124 Parma, Italy
| | - Francesca Zimetti
- Department of Food and Drug, Università degli Studi di Parma, 43124 Parma, Italy
| | - Vincenza Dolo
- Department of Life, Health and Environmental Sciences, Università degli Studi dell'Aquila, 67100 L'Aquila, Italy
| | - Cristina Banfi
- Centro Cardiologico Monzino, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), 20133 Milan, Italy
| | - Nicola Ferri
- Department of Medicine, Università degli Studi di Padova, 35100 Padua, Italy
| | - Cesare R Sirtori
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, 20133 Milan, Italy
| | - Alberto Corsini
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, 20133 Milan, Italy
| | - Silvia Stella Barbieri
- Centro Cardiologico Monzino, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), 20133 Milan, Italy
| | - Anna Pistocchi
- Department of Medical Biotechnology and Translational, Università degli Studi di Milano, L.I.T.A., 20133 Milan, Italy
| | - Valentina Bollati
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, 20133 Milan, Italy
| | - Chiara Macchi
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, 20133 Milan, Italy
| | - Massimiliano Ruscica
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, 20133 Milan, Italy
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4
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Prenylcysteine Oxidase 1 (PCYOX1), a New Player in Thrombosis. Int J Mol Sci 2022; 23:ijms23052831. [PMID: 35269975 PMCID: PMC8911005 DOI: 10.3390/ijms23052831] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 02/04/2023] Open
Abstract
Prenylcysteine Oxidase 1 (PCYOX1) is an enzyme involved in the degradation of prenylated proteins. It is expressed in different tissues including vascular and blood cells. We recently showed that the secretome from Pcyox1-silenced cells reduced platelet adhesion both to fibrinogen and endothelial cells, suggesting a potential contribution of PCYOX1 into thrombus formation. Here, we show that in vivo thrombus formation after FeCl3 injury of the carotid artery was delayed in Pcyox1−/− mice, which were also protected from collagen/epinephrine induced thromboembolism. The Pcyox1−/− mice displayed normal blood cells count, vascular procoagulant activity and plasma fibrinogen levels. Deletion of Pcyox1 reduced the platelet/leukocyte aggregates in whole blood, as well as the platelet aggregation, the alpha granules release, and the αIIbβ3 integrin activation in platelet-rich plasma, in response to adenosine diphosphate (ADP) or thrombin receptor agonist peptide (TRAP). Washed platelets from the Pcyox1−/− and WT animals showed similar phosphorylation pathway activation, adhesion ability and aggregation. The presence of Pcyox1−/− plasma impaired agonist-induced WT platelet aggregation. Our findings show that the absence of PCYOX1 results in platelet hypo-reactivity and impaired arterial thrombosis, and indicates that PCYOX1 could be a novel target for antithrombotic drugs.
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Laser Capture Microdissection in the Spatial Analysis of Epigenetic Modifications in Skin: A Comprehensive Review. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:4127238. [PMID: 35186184 PMCID: PMC8850045 DOI: 10.1155/2022/4127238] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/29/2021] [Accepted: 12/24/2021] [Indexed: 12/15/2022]
Abstract
Each cell in the body contains an intricate regulation for the expression of its relevant DNA. While every cell in a multicellular organism contains identical DNA, each tissue-specific cell expresses a different set of active genes. This organizational property exists in a paradigm that is largely controlled by forces external to the DNA sequence via epigenetic regulation. DNA methylation and chromatin modifications represent some of the classical epigenetic modifications that control gene expression. Complex tissues like skin consist of heterogeneous cell types that are spatially distributed and mixed. Furthermore, each individual skin cell has a unique response to physiological and pathological cues. As such, it is difficult to classify skin tissue as homogenous across all cell types and across different environmental exposures. Therefore, it would be prudent to isolate targeted tissue elements prior to any molecular analysis to avoid a possibility of confounding the sample with unwanted cell types. Laser capture microdissection (LCM) is a powerful technique used to isolate a targeted cell group with extreme microscopic precision. LCM presents itself as a solution to tackling the problem of tissue heterogeneity in molecular analysis. This review will cover an overview of LCM technology, the principals surrounding its application, and benefits of its application to the newly defined field of epigenomics, in particular of cutaneous pathology. This presents a comprehensive review about LCM and its use in the spatial analysis of skin epigenetics. Within the realm of skin pathology, this ability to isolate tissues under specific environmental stresses, such as oxidative stress, allows a far more focused investigation.
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Alexovič M, Sabo J, Longuespée R. Microproteomic sample preparation. Proteomics 2021; 21:e2000318. [PMID: 33547857 DOI: 10.1002/pmic.202000318] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/23/2021] [Accepted: 01/27/2021] [Indexed: 12/11/2022]
Abstract
Multiple applications of proteomics in life and health science, pathology and pharmacology, require handling size-limited cell and tissue samples. During proteomic sample preparation, analyte loss in these samples arises when standard procedures are used. Thus, specific considerations have to be taken into account for processing, that are summarised under the term microproteomics (μPs). Microproteomic workflows include: sampling (e.g., flow cytometry, laser capture microdissection), sample preparation (possible disruption of cells or tissue pieces via lysis, protein extraction, digestion in bottom-up approaches, and sample clean-up) and analysis (chromatographic or electrophoretic separation, mass spectrometric measurements and statistical/bioinformatic evaluation). All these steps must be optimised to reach wide protein dynamic ranges and high numbers of identifications. Under optimal conditions, sampling is adapted to the studied sample types and nature, sample preparation isolates and enriches the whole protein content, clean-up removes salts and other interferences such as detergents or chaotropes, and analysis identifies as many analytes as the instrumental throughput and sensitivity allow. In the suggested review, we present and discuss the current state in μP applications for processing of small number of cells (cell μPs) and microscopic tissue regions (tissue μPs).
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Affiliation(s)
- Michal Alexovič
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P.J. Šafárik in Košice, Košice, Slovakia
| | - Ján Sabo
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P.J. Šafárik in Košice, Košice, Slovakia
| | - Rémi Longuespée
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
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7
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Amadeo F, Barbuto M, Bernava G, Savini N, Brioschi M, Rizzi S, Banfi C, Polvani G, Pesce M. Culture Into Perfusion-Assisted Bioreactor Promotes Valve-Like Tissue Maturation of Recellularized Pericardial Membrane. Front Cardiovasc Med 2020; 7:80. [PMID: 32478099 PMCID: PMC7235194 DOI: 10.3389/fcvm.2020.00080] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/15/2020] [Indexed: 11/13/2022] Open
Abstract
Derivation of tissue-engineered valve replacements is a strategy to overcome the limitations of the current valve prostheses, mechanical, or biological. In an effort to set living pericardial material for aortic valve reconstruction, we have previously assessed the efficiency of a recellularization strategy based on a perfusion system enabling mass transport and homogenous distribution of aortic valve-derived "interstitial" cells inside decellularized pericardial material. In the present report, we show that alternate perfusion promoted a rapid growth of valve cells inside the pericardial material and the activity of a proliferation-supporting pathway, likely controlled by the YAP transcription factor, a crucial component of the Hippo-dependent signaling cascade, especially between 3 and 14 days of culture. Quantitative mass spectrometry analysis of protein content in the tissue constructs showed deposition of valve proteins in the decellularized pericardium with a high variability at day 14 and a reproducible tissue maturation at 21 days. These results represent a step forward in the definition of strategies to produce a fully engineered tissue for replacing the calcified leaflets of failing aortic valves.
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Affiliation(s)
- Francesco Amadeo
- Unità di Ingegneria Tissutale Cardiovascolare, Centro Cardiologico Monzino, IRCCS, Milan, Italy
| | - Marianna Barbuto
- Unità di Ingegneria Tissutale Cardiovascolare, Centro Cardiologico Monzino, IRCCS, Milan, Italy
| | - Giacomo Bernava
- Unità di Ingegneria Tissutale Cardiovascolare, Centro Cardiologico Monzino, IRCCS, Milan, Italy
| | - Nicla Savini
- Unità di Ingegneria Tissutale Cardiovascolare, Centro Cardiologico Monzino, IRCCS, Milan, Italy
| | - Maura Brioschi
- Unità di Proteomica, Centro Cardiologico Monzino, IRCCS, Milan, Italy
| | - Stefano Rizzi
- Unità di Ingegneria Tissutale Cardiovascolare, Centro Cardiologico Monzino, IRCCS, Milan, Italy
| | - Cristina Banfi
- Unità di Proteomica, Centro Cardiologico Monzino, IRCCS, Milan, Italy
| | - Gianluca Polvani
- Dipartimento di Scienze Cliniche e di Comunità, Università degli studi di Milano, Milan, Italy
| | - Maurizio Pesce
- Unità di Ingegneria Tissutale Cardiovascolare, Centro Cardiologico Monzino, IRCCS, Milan, Italy
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8
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Loganathan J, Pandey R, Ambhore NS, Borowicz P, Sathish V. Laser-capture microdissection of murine lung for differential cellular RNA analysis. Cell Tissue Res 2019; 376:425-432. [PMID: 30710174 PMCID: PMC6534428 DOI: 10.1007/s00441-019-02995-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/15/2019] [Indexed: 12/11/2022]
Abstract
The lung tissue contains a heterogeneous milieu of bronchioles, epithelial, airway smooth muscle (ASM), alveolar, and immune cell types. Healthy bronchiole comprises epithelial cells surrounded by ASM cells and helps in normal respiration. In contrast, airway remodeling, or plasticity, increases surrounding of bronchial epithelium during inflammation, especially in asthmatic condition. Given the profound functional difference between ASM, epithelial, and other cell types in the lung, it is imperative to separate and isolate different cell types of lungs for genomics, proteomics, and molecular analysis, which will improve the diagnostic and therapeutic approach to treat cell-specific lung disorders. Laser capture microdissection (LCM) is the technique generally used for the isolation of specific cell populations under direct visual inspection, which plays a crucial role to evaluate cell-specific effect in clinical and preclinical setup. However, maintenance of tissue RNA quality and integrity in LCM studies are very challenging tasks. It is obvious to believe that the major factor affecting the RNA quality is tissue-fixation method. The prime focus of this study was to address the RNA quality factors within the lung tissue using the different solvent system to fix tissue sample to obtain high-quality RNA. Paraformaldehyde and Carnoy's solutions were used for fixing the lung tissue and compared RNA integrity in LCM captured lung tissue samples. To further confirm the quality of RNA, we measured cellular marker genes in collected lung tissue samples from control and mixed allergen (MA)-induced asthmatic mouse model using qRT-PCR technique. RNA integrity number showed a significantly better quality of RNA in lung tissue samples fixed with Carnoy's solution compared to paraformaldehyde solution. Isolated RNA from MA-induced asthmatic murine lung epithelium, smooth muscle, and granulomatous foci using LCM showed a significant increase in remodeling gene expression compared to control which confirm the quality and integrity of isolated RNA. Overall, the study concludes tissue fixation solvent can alter the quality of RNA in the lung and the outcome of the results.
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Affiliation(s)
- Jagadish Loganathan
- Department of Pharmaceutical Sciences, School of Pharmacy, North Dakota State University, Sudro Hall, Room 203, Fargo, ND, 58108-6050, USA
| | - Roshni Pandey
- Department of Pharmaceutical Sciences, School of Pharmacy, North Dakota State University, Sudro Hall, Room 203, Fargo, ND, 58108-6050, USA
| | - Nilesh Sudhakar Ambhore
- Department of Pharmaceutical Sciences, School of Pharmacy, North Dakota State University, Sudro Hall, Room 203, Fargo, ND, 58108-6050, USA
| | - Pawel Borowicz
- Department of Animal Sciences, North Dakota State University, Fargo, ND, USA
| | - Venkatachalem Sathish
- Department of Pharmaceutical Sciences, School of Pharmacy, North Dakota State University, Sudro Hall, Room 203, Fargo, ND, 58108-6050, USA.
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9
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Banfi C, Brioschi M, Karjalainen MK, Huusko JM, Gianazza E, Agostoni P. Immature surfactant protein-B impairs the antioxidant capacity of HDL. Int J Cardiol 2019; 285:53-58. [PMID: 30857841 DOI: 10.1016/j.ijcard.2019.02.057] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 02/19/2019] [Accepted: 02/25/2019] [Indexed: 11/30/2022]
Abstract
Circulating immature surfactant protein B (proSP-B) forms emerged as the most reliable lung-specific circulating marker for alveolar-capillary membrane (ACM) dysfunction and for the overall clinical status of heart failure (HF). Notably, in terms of HF hospitalization, immature SP-B overwhelms the prognostic role of other most frequently used clinical parameters such as those related to lung dysfunction. The strong prognostic value of circulating proSP-B in HF suggests more widespread and possible systemic effects. Thus, we assessed the plasma distribution of proSP-B evaluating whether it exists in a lipoprotein-bound form and its impact on lipoprotein structure and function. ProSP-B forms were detectable in high-density lipoprotein (HDL) only. To assess the impact of proSP-B on HDL, HDL from healthy subjects were enriched with proSP-B produced by a stably transfected CHO cell line that specifically expresses and releases the human proSP-B. After enrichment, HDL size and lipoprotein electrophoretic mobility, and protein composition did not show apparent differences. HDL antioxidant capacity (HOI), assessed as their ability to inhibit air-induced LDL oxidation, was impaired after proSP-B enrichment. HOI was also higher in HF patients with respect to age-matched control healthy subjects (p = 0.013). Circulating proSP-B, besides its potential role as a specific marker for ACM dysfunction in HF patients with diagnostic and prognostic value, binds to human HDL impairing their antioxidant capacity. These findings shed light on proSP-B as a molecule that contributes to the reduction of the defense against oxidative stress, a key mediator in the pathogenesis of HF.
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Affiliation(s)
| | | | - Minna K Karjalainen
- PEDEGO Research Unit, Medical Research Center Oulu, University of Oulu, Oulu, Finland; Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | - Johanna M Huusko
- PEDEGO Research Unit, Medical Research Center Oulu, University of Oulu, Oulu, Finland; Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | | | - Piergiuseppe Agostoni
- Centro Cardiologico Monzino, IRCCS, Milano, Italy; Dipartimento di Scienze Cliniche e di Comunità, Sezione Cardiovascolare, Università di Milano, Italy
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10
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Pontremoli M, Brioschi M, Baetta R, Ghilardi S, Banfi C. Identification of DKK-1 as a novel mediator of statin effects in human endothelial cells. Sci Rep 2018; 8:16671. [PMID: 30420710 PMCID: PMC6232108 DOI: 10.1038/s41598-018-35119-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 10/29/2018] [Indexed: 12/18/2022] Open
Abstract
This study shows that DKK-1, a member of the Dickkopf family and a regulator of the Wnt pathways, represents a novel target of statins which, through the inhibition of HMG-CoA reductase and of non-steroidal isoprenoid intermediates, exert extra-beneficial effect in preventing atherosclerosis beyond their effect on the lipid profile. We found that atorvastatin downregulates DKK-1 protein (−88.3 ± 4.1%) and mRNA expression (−90 ± 4.2%) through the inhibition of Cdc42, Rho and Rac geranylgeranylated proteins. Further, a combined approach based on the integration of label-free quantitative mass spectrometry based-proteomics and gene silencing allowed us to demonstrate that DKK-1 itself mediates, at least in part, statin effects on human endothelial cells. Indeed, DKK-1 is responsible for the regulation of the 21% of the statin-modulated proteins, which include, among others, clusterin/apoJ, plasminogen activator inhibitor type 1 (PAI-1), myristoylated alanine-rich C-kinase substrate (MARCKS), and pentraxin 3 (PTX3). The Gene Ontology enrichment annotation revealed that DKK-1 is also a potential mediator of the extracellular matrix organization, platelet activation and response to wounding processes induced by statin. Finally, we found that plasma level of DKK-1 from cholesterol-fed rabbits treated with atorvastatin (2.5 mg/kg/day for 8 weeks) was lower (−42 ± 23%) than that of control animals. Thus, DKK-1 is not only a target of statin but it directly regulates the expression of molecules involved in a plethora of biological functions, thus expanding its role, which has been so far restricted mainly to cancer.
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11
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Santoro R, Venkateswaran S, Amadeo F, Zhang R, Brioschi M, Callanan A, Agrifoglio M, Banfi C, Bradley M, Pesce M. Acrylate-based materials for heart valve scaffold engineering. Biomater Sci 2018; 6:154-167. [PMID: 29148548 DOI: 10.1039/c7bm00854f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Calcific aortic valve disease (CAVD) is the most frequent cardiac valve pathology. Its standard treatment consists of surgical replacement either with mechanical (metal made) or biological (animal tissue made) valve prostheses, both of which have glaring deficiencies. In the search for novel materials to manufacture artificial valve tissue, we have conducted a high-throughput screening with subsequent up-scaling to identify non-degradable polymer substrates that promote valve interstitial cells (VICs) adherence/growth and, at the same time, prevent their evolution toward a pro-calcific phenotype. Here, we provide evidence that one of the two identified 'hit' polymers, poly(methoxyethylmethacrylate-co-diethylaminoethylmethacrylate), provided robust VICs adhesion and maintained the healthy VICs phenotype without inducing pro-osteogenic differentiation. This ability was also maintained when the polymer was used to coat a non-woven poly-caprolactone (PCL) scaffold using a novel solvent coating procedure, followed by bioreactor-assisted VICs seeding. Since we observed that VICs had an increased secretion of the elastin-maturing component MFAP4 in addition to other valve-specific extracellular matrix components, we conclude that valve implants constructed with this polyacrylate will drive the biological response of human valve-specific cells.
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Affiliation(s)
- Rosaria Santoro
- Unità di Ingegneria Tissutale Cardiovascolare, Centro Cardiologico Monzino, IRCCS, Milan, Italy.
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12
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Amadeo F, Boschetti F, Polvani G, Banfi C, Pesce M, Santoro R. Aortic valve cell seeding into decellularized animal pericardium by perfusion-assisted bioreactor. J Tissue Eng Regen Med 2018; 12:1481-1493. [PMID: 29702745 DOI: 10.1002/term.2680] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 02/28/2018] [Accepted: 04/16/2018] [Indexed: 12/19/2022]
Abstract
Animal-derived pericardium is the elective tissue employed in manufacturing heart valve prostheses. The preparation of this tissue for biological valve production consists of fixation with aldehydes, which reduces, but not eliminates, the xenoantigens and the donor cellular material. As a consequence, especially in patients below 65-70 years of age, the employment of valve substitutes contaning pericardium is not indicated due to progressive calcification that causes tissue degeneration and recurrence of valve insufficiency. Decellularization with ionic or nonionic detergents has been proposed as an alternative procedure to prepare aldehyde- or xenoantigen-free pericardium for biological valve manufacturing. In the present contribution, we optimized a decellularization procedure that is permissive for seeding and culturing valve competent cells able to colonize and reconstitute a valve-like tissue. A high-efficiency cellularization was achieved by forcing cell penetration inside the pericardium matrix using a perfusion bioreactor. Because the decellularization procedure was found not to alter the collagen composition of the pericardial matrix and cells seeded in the tissue constructs consistently grew and acquired the phenotype of "quiescent" valve interstitial cells, our investigation sets a novel standard in pericardium application for tissue engineering of "living" valve implants.
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Affiliation(s)
- Francesco Amadeo
- Unità di Ingegneria Tissutale Cardiovascolare, Centro Cardiologico Monzino IRCCS, Milan, Italy
| | | | - Gianluca Polvani
- Dipartimento di Scienze Cliniche e di Comunità, Università di Milano, Milan, Italy
| | - Cristina Banfi
- Unità di Proteomica, Centro Cardiologico Monzino IRCCS, Milan, Italy
| | - Maurizio Pesce
- Unità di Ingegneria Tissutale Cardiovascolare, Centro Cardiologico Monzino IRCCS, Milan, Italy
| | - Rosaria Santoro
- Unità di Ingegneria Tissutale Cardiovascolare, Centro Cardiologico Monzino IRCCS, Milan, Italy
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Gordon A, Kannan SK, Gousset K. A Novel Cell Fixation Method that Greatly Enhances Protein Identification in Microproteomic Studies Using Laser Capture Microdissection and Mass Spectrometry. Proteomics 2018; 18:e1700294. [PMID: 29579344 DOI: 10.1002/pmic.201700294] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 12/21/2017] [Indexed: 11/05/2022]
Abstract
Microproteomic studies have improved our knowledge of cell biology. Yet, with mass spectrometry (MS) analysis, accuracy can be lost for protein identification and quantification when using heterogeneous samples. Laser capture microdissection (LCM) allows for the enrichment of specific subsets of cells to study their proteome; however, sample fixation is necessary. Unfortunately, fixation hampers MS results due to protein cross-linking. The aim of this study was to identify both a fixation protocol and an extraction method that returns the best yield of proteins for downstream MS analysis, while preserving cellular structures. We compared glutaraldehyde (GLU), a common fixative to preserve cells, to dithiobispropionimidate (DTBP), a cleavable cross-linker. Our DTBP fixation/extraction protocol greatly increased the protein recovery. In fact, while 1000 GLU fixed cells returned only 159 unique protein hits, from 1464 unique peptides of 1994 unique collected spectra, 1000 DTBP fixed cells resulted in 567 unique collected protein hits, from 7542 unique peptides, of 10,401 unique collected spectra. That is, a 3.57-fold increase in protein hits, 5.15-fold increase in unique peptides, and a 5.22-fold increase in unique collected spectra. Overall, the novel protocol introduced here allows for a very efficient protein recovery and good sample quality for MS after sample collection using LCM.
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Affiliation(s)
- Ana Gordon
- Biology Department, California State University Fresno, 2555 East San Ramon Ave M/S SB73, Fresno, CA, 93740, USA
| | - Shravan Kumar Kannan
- Biology Department, California State University Fresno, 2555 East San Ramon Ave M/S SB73, Fresno, CA, 93740, USA
| | - Karine Gousset
- Biology Department, California State University Fresno, 2555 East San Ramon Ave M/S SB73, Fresno, CA, 93740, USA
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14
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Mourino-Alvarez L, Baldan-Martin M, Rincon R, Martin-Rojas T, Corbacho-Alonso N, Sastre-Oliva T, Barderas MG. Recent advances and clinical insights into the use of proteomics in the study of atherosclerosis. Expert Rev Proteomics 2017; 14:701-713. [PMID: 28689450 DOI: 10.1080/14789450.2017.1353912] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION The application of new proteomics methods may help to identify new diagnostic/predictive molecular markers in an attempt to improve the clinical management of atherosclerosis. Areas covered: Technological advances in proteomics have enhanced its sensitivity and multiplexing capacity, as well as the possibility of studying protein interactions and tissue structure. These advances will help us better understand the molecular mechanisms at play in atherosclerosis as a biological system. Moreover, this should help identify new predictive/diagnostic biomarkers and therapeutic targets that may facilitate effective risk stratification and early diagnosis, with the ensuing rapid implementation of treatment. This review provides a comprehensive overview of the novel methods in proteomics, including state-of-the-art techniques, novel biological samples and applications for the study of atherosclerosis. Expert commentary: Collaboration between clinicians and researchers is crucial to further validate and introduce new molecular markers to manage atherosclerosis that are identified using the most up to date proteomic approaches.
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Affiliation(s)
- Laura Mourino-Alvarez
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
| | | | - Raul Rincon
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
| | - Tatiana Martin-Rojas
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
| | - Nerea Corbacho-Alonso
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
| | - Tamara Sastre-Oliva
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
| | - Maria G Barderas
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
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15
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Brioschi M, Baetta R, Ghilardi S, Gianazza E, Guarino A, Parolari A, Polvani G, Tremoli E, Banfi C. Normal human mitral valve proteome: A preliminary investigation by gel-based and gel-free proteomic approaches. Electrophoresis 2016; 37:2633-2643. [PMID: 27450324 DOI: 10.1002/elps.201600081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 06/27/2016] [Accepted: 07/14/2016] [Indexed: 12/24/2022]
Abstract
The mitral valve is a highly complex structure which regulates blood flow from the left atrium to the left ventricle (LV) avoiding a significant forward gradient during diastole or regurgitation during systole. The integrity of the mitral valve is also essential for the maintenance of normal LV size, geometry, and function. Significant advances in the comprehension of the biological, functional, and mechanical behavior of the mitral valve have recently been made. However, current knowledge of protein components in the normal human mitral valve is still limited and complicated by the low cellularity of this tissue and the presence of high abundant proteins from the extracellular matrix. We employed here an integrated proteomic approach to analyse the protein composition of the normal human mitral valve and reported confident identification of 422 proteins, some of which have not been previously described in this tissue. In particular, we described the ability of pre-MS separation technique based on liquid-phase IEF and SDS-PAGE to identify the largest number of proteins. We also demonstrated that some of these proteins, e.g. αB-Crystallin, septin-11, four-and-a-half LIM domains protein 1, and dermatopontin, are synthesised by interstitial cells isolated from human mitral valves. These initial results provide a valuable basis for future studies aimed at analysing in depth the mitral valve protein composition and at investigating potential pathogenetic molecular mechanisms. Data are available via ProteomeXchange with identifier PXD004397.
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Affiliation(s)
| | | | | | | | - Anna Guarino
- Centro Cardiologico Monzino, IRCCS, Milan, Italy.,Banca Tessuti Cardiovascolari Regione Lombardia, Centro Cardiologico Monzino IRCCS Milan, Milan, Italy
| | - Alessandro Parolari
- Dipartimento di Chirurgia cardiaca, IRCCS Policlinico San Donato, Milan, Italy
| | - Gianluca Polvani
- Centro Cardiologico Monzino, IRCCS, Milan, Italy.,Università degli Studi di Milano, Dipartimento di Scienze Cliniche e di Comunità, Sezione Cardiovascolare, Milan, Italy
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16
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Roverso M, Brioschi M, Banfi C, Visentin S, Burlina S, Seraglia R, Traldi P, Lapolla A. A preliminary study on human placental tissue impaired by gestational diabetes: a comparison of gel-based versus gel-free proteomics approaches. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2016; 22:71-82. [PMID: 27419900 DOI: 10.1255/ejms.1412] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Gestational diabetes (GDM) is the most common complication of pregnancy and it is associated with maternal and fetal short- and long-term consequences. GDM modifies placental structure and function, but many of the underlying mechanisms are still unclear. The aim of this study is to develop and compare two different methods, based respectively on gel-based and gel-free proteomics, in order to investigate the placental proteome in the absence or in the presence of GDM and to identify, through a comparative approach, possible changes in protein expression due to the GDM condition. Placenta homogenates obtained by pooling six control samples and six samples from GDM pregnant women were analyzed by two-dimensional (2D) electrophoresis coupled with mass spectrometry [nano-liquid chromatography (nano-LC) tandem mass spectrometry (MS/MS) and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS)] and by a label-free mass spectrometry method based on LC-MS(E). The gel-based approach highlights 13 over-expressed proteins and 16 under-expressed proteins, while the label-free method shows the over- expression of 10 proteins and the under-expression of nine proteins. As regards 2D gel electrophoresis, a comparison between two different protein identification methods, based respectively on nLC-electrospray ionization-MS/MS and MALDI-MS/MS, was performed taking into consideration the sequence coverage, the MASCOT score and the exponentially modified protein abundance index. The analysis of the complex proteome through an integrated strategy revealed that the quantitative gel-free and label-free MS approach might be suitable to identify candidate markers of GDM.
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Affiliation(s)
- Marco Roverso
- Department of Medicine, University of Padova, via Giustiniani 2, 35128 Padova, Italy. Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy.
| | - Maura Brioschi
- Centro Cardiologico Monzino I.R.C.C.S, Via Parea 4, Milan, Italy.
| | - Cristina Banfi
- Centro Cardiologico Monzino I.R.C.C.S, Via Parea 4, Milan, Italy.
| | - Silvia Visentin
- Department of Woman's and Child's Health, University of Padova, via Giustiniani 2, 35128 Padova, Italy.
| | - Silvia Burlina
- Department of Medicine, University of Padova, via Giustiniani 2, 35128 Padova, Italy.
| | | | | | - Annunziata Lapolla
- Department of Medicine, University of Padova, via Giustiniani 2, 35128 Padova, Italy.
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17
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Datta S, Malhotra L, Dickerson R, Chaffee S, Sen CK, Roy S. Laser capture microdissection: Big data from small samples. Histol Histopathol 2015; 30:1255-69. [PMID: 25892148 PMCID: PMC4665617 DOI: 10.14670/hh-11-622] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Any tissue is made up of a heterogeneous mix of spatially distributed cell types. In response to any (patho) physiological cue, responses of each cell type in any given tissue may be unique and cannot be homogenized across cell-types and spatial co-ordinates. For example, in response to myocardial infarction, on one hand myocytes and fibroblasts of the heart tissue respond differently. On the other hand, myocytes in the infarct core respond differently compared to those in the peri-infarct zone. Therefore, isolation of pure targeted cells is an important and essential step for the molecular analysis of cells involved in the progression of disease. Laser capture microdissection (LCM) is powerful to obtain a pure targeted cell subgroup, or even a single cell, quickly and precisely under the microscope, successfully tackling the problem of tissue heterogeneity in molecular analysis. This review presents an overview of LCM technology, the principles, advantages and limitations and its down-stream applications in the fields of proteomics, genomics and transcriptomics. With powerful technologies and appropriate applications, this technique provides unprecedented insights into cell biology from cells grown in their natural tissue habitat as opposed to those cultured in artificial petri dish conditions.
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Affiliation(s)
- Soma Datta
- Department of Surgery, Center for Regenerative Medicine and Cell Based Therapies and Comprehensive Wound Center, Laser Capture Molecular Core, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Lavina Malhotra
- Department of Surgery, Center for Regenerative Medicine and Cell Based Therapies and Comprehensive Wound Center, Laser Capture Molecular Core, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Ryan Dickerson
- Department of Surgery, Center for Regenerative Medicine and Cell Based Therapies and Comprehensive Wound Center, Laser Capture Molecular Core, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Scott Chaffee
- Department of Surgery, Center for Regenerative Medicine and Cell Based Therapies and Comprehensive Wound Center, Laser Capture Molecular Core, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Chandan K Sen
- Department of Surgery, Center for Regenerative Medicine and Cell Based Therapies and Comprehensive Wound Center, Laser Capture Molecular Core, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Sashwati Roy
- Department of Surgery, Center for Regenerative Medicine and Cell Based Therapies and Comprehensive Wound Center, Laser Capture Molecular Core, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA.
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Data for proteomic analysis of murine cardiomyocytic HL-1 cells treated with siRNA against tissue factor. Data Brief 2015. [PMID: 26217730 PMCID: PMC4510070 DOI: 10.1016/j.dib.2015.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
This data article is related to the research article entitled Proteomics of Tissue Factor silencing in cardiomyocytic cells reveals a new role for this coagulation factor in splicing machinery control by Lento et al. [1]. Tissue Factor (TF) is a key player in the coagulation cascade, but it has additional functions ranging from angiogenesis, tumour invasion and, in the heart, the maintenance of the integrity of cardiac cells. This article reports the nano-LC-MS(E) analysis of the cardiomyocytic HL-1 cell line proteome and describes the results obtained from a Gene Ontology analysis of those proteins affected by TF-gene silencing.
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19
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Eligini S, Brioschi M, Fiorelli S, Tremoli E, Banfi C, Colli S. Human monocyte-derived macrophages are heterogenous: Proteomic profile of different phenotypes. J Proteomics 2015; 124:112-23. [DOI: 10.1016/j.jprot.2015.03.026] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 03/13/2015] [Accepted: 03/29/2015] [Indexed: 12/25/2022]
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20
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Eligini S, Brioschi M, Fiorelli S, Tremoli E, Colli S, Banfi C. Data for proteomic analysis of Human monocyte-derived macrophages. Data Brief 2015. [PMID: 26217784 PMCID: PMC4510452 DOI: 10.1016/j.dib.2015.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
This data article is referred to the research article entitled Human monocyte-derived macrophages are heterogeneous: proteomic profile of different phenotypes by Eligini et al. Eligini S., Brioschi M., Fiorelli S., Tremoli E., Banfi C., Colli S. Human monocyte-derived macrophages are heterogeneous: proteomic profile of different phenotypes. J. Proteomics 124, 2015, 112-123. Macrophages obtained in vitro from blood monocytes are largely used as surrogate model of tissue macrophages that are heterogeneous and not easy to obtain and handle. Under spontaneous differentiation in vitro, monocyte-derived macrophages (MDMs) display two dominant subsets (round and spindle) that show different transcriptional, antigenic, and functional profiles mimicking, at least in part, the heterogeneity of tissue macrophages. This article reports the nano-LC-MSE analysis of the proteome of round and spindle MDMs allowing a deeper comprehension of macrophage heterogeneity.
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Affiliation(s)
- S Eligini
- Centro Cardiologico Monzino I.R.C.C.S, Milan, Italy
| | - M Brioschi
- Centro Cardiologico Monzino I.R.C.C.S, Milan, Italy
| | - S Fiorelli
- Centro Cardiologico Monzino I.R.C.C.S, Milan, Italy
| | - E Tremoli
- Centro Cardiologico Monzino I.R.C.C.S, Milan, Italy ; Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - S Colli
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - C Banfi
- Centro Cardiologico Monzino I.R.C.C.S, Milan, Italy
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21
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Lento S, Brioschi M, Barcella S, Nasim MT, Ghilardi S, Barbieri SS, Tremoli E, Banfi C. Proteomics of tissue factor silencing in cardiomyocytic cells reveals a new role for this coagulation factor in splicing machinery control. J Proteomics 2015; 119:75-89. [DOI: 10.1016/j.jprot.2015.01.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 01/08/2015] [Accepted: 01/25/2015] [Indexed: 12/12/2022]
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22
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Groh KJ, Suter MJF. Stressor-induced proteome alterations in zebrafish: a meta-analysis of response patterns. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2015; 159:1-12. [PMID: 25498419 DOI: 10.1016/j.aquatox.2014.11.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Revised: 11/05/2014] [Accepted: 11/18/2014] [Indexed: 06/04/2023]
Abstract
Proteomics approaches are being increasingly applied in ecotoxicology on the premise that the identification of specific protein expression changes in response to a particular chemical would allow elucidation of the underlying molecular pathways leading to an adverse effect. This in turn is expected to promote the development of focused testing strategies for specific groups of toxicants. Although both gel-based and gel-free global characterization techniques provide limited proteome coverage, the conclusions regarding the cellular processes affected are still being drawn based on the few changes detected. To investigate how specific the detected responses are, we analyzed a set of studies that characterized proteome alterations induced by various physiological, chemical and biological stressors in zebrafish, a popular model organism. Our analysis highlights several proteins and protein groups, including heat shock and oxidative stress defense proteins, energy metabolism enzymes and cytoskeletal proteins, to be most frequently identified as responding to diverse stressors. In contrast, other potentially more specifically responding protein groups are detected much less frequently. Thus, zebrafish proteome responses to stress reported by different studies appear to depend mostly on the level of stress rather than on the specific stressor itself. This suggests that the most broadly used current proteomics technologies do not provide sufficient proteome coverage to allow in-depth investigation of specific mechanisms of toxicant action. We suggest that the results of any differential proteomics experiment performed with zebrafish should be interpreted keeping in mind the list of the most frequent responders that we have identified. Similar reservations should apply to any other species where proteome responses are analyzed by global proteomics methods. Careful consideration of the reliability and significance of observed changes is necessary in order not to over-interpret the experimental results and to prevent the proliferation of false positive linkages between the chemical and the cellular functions it perturbs. We further discuss the implications of the identified "top lists" of frequently responding proteins and protein families, and suggest further directions for proteomics research in ecotoxicology. Apart from improving the proteome coverage, further research should focus on defining the significance of the observed stress response patterns for organism phenotypes and on searching for common upstream regulators that can be targeted by specific assays.
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Affiliation(s)
- Ksenia J Groh
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland; ETH Zürich, Swiss Federal Institute of Technology, Department of Chemistry and Applied Biosciences, 8093 Zürich, Switzerland.
| | - Marc J-F Suter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland; ETH Zürich, Swiss Federal Institute of Technology, Department of Environmental Systems Science, 8092 Zürich, Switzerland
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