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Holub M, Birnie A, Japaridze A, van der Torre J, Ridder MD, de Ram C, Pabst M, Dekker C. Extracting and characterizing protein-free megabase-pair DNA for in vitro experiments. CELL REPORTS METHODS 2022; 2:100366. [PMID: 36590691 PMCID: PMC9795359 DOI: 10.1016/j.crmeth.2022.100366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/29/2022] [Accepted: 11/16/2022] [Indexed: 12/15/2022]
Abstract
Chromosome structure and function is studied using various cell-based methods as well as with a range of in vitro single-molecule techniques on short DNA substrates. Here, we present a method to obtain megabase-pair-length deproteinated DNA for in vitro studies. We isolated chromosomes from bacterial cells and enzymatically digested the native proteins. Mass spectrometry indicated that 97%-100% of DNA-binding proteins are removed from the sample. Fluorescence microscopy analysis showed an increase in the radius of gyration of the DNA polymers, while the DNA length remained megabase-pair sized. In proof-of-concept experiments using these deproteinated long DNA molecules, we observed DNA compaction upon adding the DNA-binding protein Fis or PEG crowding agents and showed that it is possible to track the motion of a fluorescently labeled DNA locus. These results indicate the practical feasibility of a "genome-in-a-box" approach to study chromosome organization from the bottom up.
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Affiliation(s)
- Martin Holub
- Department of Bionanoscience & Kavli Institute for Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Anthony Birnie
- Department of Bionanoscience & Kavli Institute for Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Aleksandre Japaridze
- Department of Bionanoscience & Kavli Institute for Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Jaco van der Torre
- Department of Bionanoscience & Kavli Institute for Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Maxime den Ridder
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Carol de Ram
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Cees Dekker
- Department of Bionanoscience & Kavli Institute for Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
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Perdomo L, Vidal-Gómez X, Soleti R, Vergori L, Duluc L, Chwastyniak M, Bisserier M, Le Lay S, Villard A, Simard G, Meilhac O, Lezoualc'h F, Khantalin I, Veerapen R, Dubois S, Boursier J, Henni S, Gagnadoux F, Pinet F, Andriantsitohaina R, Martínez MC. Large Extracellular Vesicle-Associated Rap1 Accumulates in Atherosclerotic Plaques, Correlates With Vascular Risks and Is Involved in Atherosclerosis. Circ Res 2020; 127:747-760. [PMID: 32539601 DOI: 10.1161/circresaha.120.317086] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
RATIONALE Metabolic syndrome (MetS) is a cluster of interrelated risk factors for cardiovascular diseases and atherosclerosis. Circulating levels of large extracellular vesicles (lEVs), submicrometer-sized vesicles released from plasma membrane, from MetS patients were shown to induce endothelial dysfunction, but their role in early stage of atherosclerosis and on vascular smooth muscle cells (SMC) remain to be fully elucidated. OBJECTIVE To determine the mechanisms by which lEVs lead to the progression of atherosclerosis in the setting of MetS. METHODS AND RESULTS Proteomic analysis revealed that the small GTPase, Rap1 was overexpressed in lEVs from MetS patients compared with those from non-MetS subjects. Rap1 was in GTP-associated active state in both types of lEVs, and Rap1-lEVs levels correlated with increased cardiovascular risks, including stenosis. MetS-lEVs, but not non-MetS-lEVs, increased Rap1-dependent endothelial cell permeability. MetS-lEVs significantly promoted migration and proliferation of human aortic SMC and increased expression of proinflammatory molecules and activation of ERK (extracellular signal-regulated kinase) 5/p38 pathways. Neutralization of Rap1 by specific antibody or pharmacological inhibition of Rap1 completely prevented the effects of lEVs from MetS patients. High-fat diet-fed ApoE-/- mice displayed an increased expression of Rap1 both in aortas and circulating lEVs. lEVs accumulated in plaque atherosclerotic lesions depending on the progression of atherosclerosis. lEVs from high-fat diet-fed ApoE-/- mice, but not those from mice fed with a standard diet, enhanced SMC proliferation. Human atherosclerotic lesions were enriched in lEVs expressing Rap1. CONCLUSIONS These data demonstrate that Rap1 carried by MetS-lEVs participates in the enhanced SMC proliferation, migration, proinflammatory profile, and activation of ERK5/p38 pathways leading to vascular inflammation and remodeling, and atherosclerosis. These results highlight that Rap1 carried by MetS-lEVs may be a novel determinant of diagnostic value for cardiometabolic risk factors and suggest Rap1 as a promising therapeutic target against the development of atherosclerosis. Graphical Abstract: A graphical abstract is available for this article.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Animals
- Atherosclerosis/blood
- Atherosclerosis/metabolism
- Atherosclerosis/pathology
- Case-Control Studies
- Cell Movement
- Cell Proliferation
- Cells, Cultured
- Disease Models, Animal
- Endothelial Cells/metabolism
- Endothelial Cells/pathology
- Extracellular Vesicles/metabolism
- Female
- Humans
- Male
- Mice, Inbred C57BL
- Mice, Knockout, ApoE
- Middle Aged
- Mitogen-Activated Protein Kinase 7/metabolism
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/pathology
- Permeability
- Phosphorylation
- Plaque, Atherosclerotic
- Prognosis
- Proteomics
- Risk Assessment
- Risk Factors
- Signal Transduction
- p38 Mitogen-Activated Protein Kinases/metabolism
- rap GTP-Binding Proteins
- rap1 GTP-Binding Proteins/metabolism
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Affiliation(s)
- Liliana Perdomo
- From the SOPAM, U1063, INSERM, UNIV Angers, SFR ICAT, France (L.P., X.V.-G., R.S., L.V., L.D., S.L.L., A.V., G.S., S.D., F.G., R.A., M.C.M.)
| | - Xavier Vidal-Gómez
- From the SOPAM, U1063, INSERM, UNIV Angers, SFR ICAT, France (L.P., X.V.-G., R.S., L.V., L.D., S.L.L., A.V., G.S., S.D., F.G., R.A., M.C.M.)
| | - Raffaella Soleti
- From the SOPAM, U1063, INSERM, UNIV Angers, SFR ICAT, France (L.P., X.V.-G., R.S., L.V., L.D., S.L.L., A.V., G.S., S.D., F.G., R.A., M.C.M.)
| | - Luisa Vergori
- From the SOPAM, U1063, INSERM, UNIV Angers, SFR ICAT, France (L.P., X.V.-G., R.S., L.V., L.D., S.L.L., A.V., G.S., S.D., F.G., R.A., M.C.M.)
| | - Lucie Duluc
- From the SOPAM, U1063, INSERM, UNIV Angers, SFR ICAT, France (L.P., X.V.-G., R.S., L.V., L.D., S.L.L., A.V., G.S., S.D., F.G., R.A., M.C.M.)
| | - Maggy Chwastyniak
- Université de Lille, Inserm, CHU Lille, Institute Pasteur De Lille, U1167 - RID-AGE, Lille, France (M.C., F.P.)
| | - Malik Bisserier
- Inserm, UMR-1048, Institut Des Maladies Métaboliques et Cardiovasculaires, Toulouse, France (M.B., F.L.)
| | - Soazig Le Lay
- From the SOPAM, U1063, INSERM, UNIV Angers, SFR ICAT, France (L.P., X.V.-G., R.S., L.V., L.D., S.L.L., A.V., G.S., S.D., F.G., R.A., M.C.M.)
| | - Alexandre Villard
- From the SOPAM, U1063, INSERM, UNIV Angers, SFR ICAT, France (L.P., X.V.-G., R.S., L.V., L.D., S.L.L., A.V., G.S., S.D., F.G., R.A., M.C.M.)
| | - Gilles Simard
- From the SOPAM, U1063, INSERM, UNIV Angers, SFR ICAT, France (L.P., X.V.-G., R.S., L.V., L.D., S.L.L., A.V., G.S., S.D., F.G., R.A., M.C.M.)
| | - Olivier Meilhac
- DéTROI, INSERM U1188, Université de La Réunion, France (O.M.)
| | - Frank Lezoualc'h
- Inserm, UMR-1048, Institut Des Maladies Métaboliques et Cardiovasculaires, Toulouse, France (M.B., F.L.)
| | | | - Reuben Veerapen
- Clinique Sainte-Clotilde, Groupe Clinifutur, Sainte-Clotilde, France (R.V.)
| | - Séverine Dubois
- From the SOPAM, U1063, INSERM, UNIV Angers, SFR ICAT, France (L.P., X.V.-G., R.S., L.V., L.D., S.L.L., A.V., G.S., S.D., F.G., R.A., M.C.M.)
- CHU d'Angers, France (S.D., J.B., S.H., F.G., R.A., M.C.M.)
| | | | - Samir Henni
- CHU d'Angers, France (S.D., J.B., S.H., F.G., R.A., M.C.M.)
| | - Frédéric Gagnadoux
- From the SOPAM, U1063, INSERM, UNIV Angers, SFR ICAT, France (L.P., X.V.-G., R.S., L.V., L.D., S.L.L., A.V., G.S., S.D., F.G., R.A., M.C.M.)
- CHU d'Angers, France (S.D., J.B., S.H., F.G., R.A., M.C.M.)
| | - Florence Pinet
- Université de Lille, Inserm, CHU Lille, Institute Pasteur De Lille, U1167 - RID-AGE, Lille, France (M.C., F.P.)
| | - Ramaroson Andriantsitohaina
- From the SOPAM, U1063, INSERM, UNIV Angers, SFR ICAT, France (L.P., X.V.-G., R.S., L.V., L.D., S.L.L., A.V., G.S., S.D., F.G., R.A., M.C.M.)
- CHU d'Angers, France (S.D., J.B., S.H., F.G., R.A., M.C.M.)
| | - M Carmen Martínez
- From the SOPAM, U1063, INSERM, UNIV Angers, SFR ICAT, France (L.P., X.V.-G., R.S., L.V., L.D., S.L.L., A.V., G.S., S.D., F.G., R.A., M.C.M.)
- CHU d'Angers, France (S.D., J.B., S.H., F.G., R.A., M.C.M.)
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Turkieh A, Fertin M, Bouvet M, Mulder P, Drobecq H, Lemesle G, Lamblin N, de Groote P, Porouchani S, Chwastyniak M, Beseme O, Amouyel P, Mouquet F, Balligand JL, Richard V, Bauters C, Pinet F. Expression and Implication of Clusterin in Left Ventricular Remodeling After Myocardial Infarction. Circ Heart Fail 2018; 11:e004838. [DOI: 10.1161/circheartfailure.117.004838] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 05/16/2018] [Indexed: 01/31/2023]
Affiliation(s)
- Annie Turkieh
- INSERM U1167-RID-AGE, CHU Lille, FHU-REMOD-VHF (A.T., M.F., M.B., N.L., P.d.G., S.P., M.C., O.B., P.A., C.B., F.P.)
| | - Marie Fertin
- INSERM U1167-RID-AGE, CHU Lille, FHU-REMOD-VHF (A.T., M.F., M.B., N.L., P.d.G., S.P., M.C., O.B., P.A., C.B., F.P.)
| | - Marion Bouvet
- INSERM U1167-RID-AGE, CHU Lille, FHU-REMOD-VHF (A.T., M.F., M.B., N.L., P.d.G., S.P., M.C., O.B., P.A., C.B., F.P.)
| | - Paul Mulder
- Institut Pasteur de Lille, Université de Lille, France. Inserm U1096, FHU-REMOD-VHF, Normandie University, University of Rouen, France (P.M., V.R.)
| | - Hervé Drobecq
- UMR 8161-M3T-Mechanisms of Tumorigenesis and Target Therapies, CNRS (H.D.)
| | - Gilles Lemesle
- USIC et Centre Hémodynamique, Institut Coeur Poumon, Centre Hospitalier Régional et Universitaire de Lille, France (G.L., N.L., P.d.G., F.M., C.B.)
- Faculté de Médecine de l’Université de Lille, France (G.L., N.L., P.A., C.B.)
- FACT, French Alliance for Cardiovascular Trials, Paris, France (G.L., N.L., C.B.)
| | - Nicolas Lamblin
- INSERM U1167-RID-AGE, CHU Lille, FHU-REMOD-VHF (A.T., M.F., M.B., N.L., P.d.G., S.P., M.C., O.B., P.A., C.B., F.P.)
- USIC et Centre Hémodynamique, Institut Coeur Poumon, Centre Hospitalier Régional et Universitaire de Lille, France (G.L., N.L., P.d.G., F.M., C.B.)
- Faculté de Médecine de l’Université de Lille, France (G.L., N.L., P.A., C.B.)
- FACT, French Alliance for Cardiovascular Trials, Paris, France (G.L., N.L., C.B.)
| | - Pascal de Groote
- INSERM U1167-RID-AGE, CHU Lille, FHU-REMOD-VHF (A.T., M.F., M.B., N.L., P.d.G., S.P., M.C., O.B., P.A., C.B., F.P.)
- USIC et Centre Hémodynamique, Institut Coeur Poumon, Centre Hospitalier Régional et Universitaire de Lille, France (G.L., N.L., P.d.G., F.M., C.B.)
| | - Sina Porouchani
- INSERM U1167-RID-AGE, CHU Lille, FHU-REMOD-VHF (A.T., M.F., M.B., N.L., P.d.G., S.P., M.C., O.B., P.A., C.B., F.P.)
| | - Maggy Chwastyniak
- INSERM U1167-RID-AGE, CHU Lille, FHU-REMOD-VHF (A.T., M.F., M.B., N.L., P.d.G., S.P., M.C., O.B., P.A., C.B., F.P.)
| | - Olivia Beseme
- INSERM U1167-RID-AGE, CHU Lille, FHU-REMOD-VHF (A.T., M.F., M.B., N.L., P.d.G., S.P., M.C., O.B., P.A., C.B., F.P.)
| | - Philippe Amouyel
- INSERM U1167-RID-AGE, CHU Lille, FHU-REMOD-VHF (A.T., M.F., M.B., N.L., P.d.G., S.P., M.C., O.B., P.A., C.B., F.P.)
- Faculté de Médecine de l’Université de Lille, France (G.L., N.L., P.A., C.B.)
- CHU Lille, Service de Santé Publique, Épidémiologie, Économie de la Santé et Prévention, France (P.A.)
| | - Frédéric Mouquet
- USIC et Centre Hémodynamique, Institut Coeur Poumon, Centre Hospitalier Régional et Universitaire de Lille, France (G.L., N.L., P.d.G., F.M., C.B.)
| | - Jean-Luc Balligand
- Institut de Recherche Experimentale et Clinique, Pole of Pharmacology and Therapeutics and Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium (J.-L.B.)
| | - Vincent Richard
- Institut Pasteur de Lille, Université de Lille, France. Inserm U1096, FHU-REMOD-VHF, Normandie University, University of Rouen, France (P.M., V.R.)
| | - Christophe Bauters
- INSERM U1167-RID-AGE, CHU Lille, FHU-REMOD-VHF (A.T., M.F., M.B., N.L., P.d.G., S.P., M.C., O.B., P.A., C.B., F.P.)
- USIC et Centre Hémodynamique, Institut Coeur Poumon, Centre Hospitalier Régional et Universitaire de Lille, France (G.L., N.L., P.d.G., F.M., C.B.)
- Faculté de Médecine de l’Université de Lille, France (G.L., N.L., P.A., C.B.)
- FACT, French Alliance for Cardiovascular Trials, Paris, France (G.L., N.L., C.B.)
| | - Florence Pinet
- INSERM U1167-RID-AGE, CHU Lille, FHU-REMOD-VHF (A.T., M.F., M.B., N.L., P.d.G., S.P., M.C., O.B., P.A., C.B., F.P.)
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Arentz G, Weiland F, Oehler MK, Hoffmann P. State of the art of 2D DIGE. Proteomics Clin Appl 2015; 9:277-88. [DOI: 10.1002/prca.201400119] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/13/2014] [Accepted: 11/10/2014] [Indexed: 02/04/2023]
Affiliation(s)
- Georgia Arentz
- School of Molecular and Biomedical Science; Adelaide Proteomics Centre; The University of Adelaide; Adelaide Australia
| | - Florian Weiland
- School of Molecular and Biomedical Science; Adelaide Proteomics Centre; The University of Adelaide; Adelaide Australia
| | - Martin K. Oehler
- School of Paediatrics and Reproductive Health; Research Centre for Reproductive Health; Robinson Institute; University of Adelaide; SA Australia
- Department of Gynaecological Oncology; Royal Adelaide Hospital; Adelaide SA Australia
| | - Peter Hoffmann
- School of Molecular and Biomedical Science; Adelaide Proteomics Centre; The University of Adelaide; Adelaide Australia
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Bouvet M, Turkieh A, Acosta-Martin AE, Chwastyniak M, Beseme O, Amouyel P, Pinet F. Proteomic profiling of macrophages by 2D electrophoresis. J Vis Exp 2014:e52219. [PMID: 25408153 DOI: 10.3791/52219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The goal of the two-dimensional (2D) electrophoresis protocol described here is to show how to analyse the phenotype of human cultured macrophages. The key role of macrophages has been shown in various pathological disorders such as inflammatory, immunological, and infectious diseases. In this protocol, we use primary cultures of human monocyte-derived macrophages that can be differentiated into the M1 (pro-inflammatory) or the M2 (anti-inflammatory) phenotype. This in vitro model is reliable for studying the biological activities of M1 and M2 macrophages and also for a proteomic approach. Proteomic techniques are useful for comparing the phenotype and behaviour of M1 and M2 macrophages during host pathogenicity. 2D gel electrophoresis is a powerful proteomic technique for mapping large numbers of proteins or polypeptides simultaneously. We describe the protocol of 2D electrophoresis using fluorescent dyes, named 2D Differential Gel Electrophoresis (DIGE). The M1 and M2 macrophages proteins are labelled with cyanine dyes before separation by isoelectric focusing, according to their isoelectric point in the first dimension, and their molecular mass, in the second dimension. Separated protein or polypeptidic spots are then used to detect differences in protein or polypeptide expression levels. The proteomic approaches described here allows the investigation of the macrophage protein changes associated with various disorders like host pathogenicity or microbial toxins.
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Acosta-Martin AE, Lane L. Combining bioinformatics and MS-based proteomics: clinical implications. Expert Rev Proteomics 2014; 11:269-84. [PMID: 24720436 DOI: 10.1586/14789450.2014.900446] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Clinical proteomics research aims at i) discovery of protein biomarkers for screening, diagnosis and prognosis of disease, ii) discovery of protein therapeutic targets for improvement of disease prevention, treatment and follow-up, and iii) development of mass spectrometry (MS)-based assays that could be implemented in clinical chemistry, microbiology or hematology laboratories. MS has been increasingly applied in clinical proteomics studies for the identification and quantification of proteins. Bioinformatics plays a key role in the exploitation of MS data in several aspects such as the generation and curation of protein sequence databases, the development of appropriate software for MS data treatment and integration with other omics data and the establishment of adequate standard files for data sharing. In this article, we discuss the main MS approaches and bioinformatics solutions that are currently applied to accomplish the objectives of clinical proteomic research.
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Beseme O, Fertin M, Drobecq H, Amouyel P, Pinet F. Combinatorial peptide ligand library plasma treatment: Advantages for accessing low-abundance proteins. Electrophoresis 2010; 31:2697-704. [PMID: 20665525 DOI: 10.1002/elps.201000188] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Depletion of major blood proteins is one of the most promising approaches to accessing low-abundance biomarkers. This study compared the use of combinatorial peptide ligand library (CPLL) and albumin and immunoglobulins (IgGs) depletion technology for accessing these low-abundance proteins in plasma using 2-DE in an acidic restricted pH range (4-7). Compared with native plasma, both techniques enlarge the visibility of other proteins than albumin and IgG, but there were marked differences in their composition. An increase of the number of spots was detected compared with native plasma (157 spots) with 427 and 557 spots, respectively, detected with albumin and IgG depletion, and CPLL treatment. We selected 70 spots to be identified by MALDI-TOF related to their absence in the 2-D gels from native or albumin and IgG-depleted plasma. The 42 spots identified corresponded to 24 different proteins, with more than half of the proteins which did not belong to the major plasma proteins. CPLL treatment allowed the accessibility to proteolytic fragments obtained from major plasma proteins. We found a large superiority of the CPLL approach over the albumin and IgG depletion process. These findings show the utility of depleting major blood proteins to be able to access low-abundance proteins and the potential of CPLL to select and identify candidate biomarkers in clinical studies.
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