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Santa C, Rodrigues JE, Martinho A, Mendes VM, Madeira N, Coroa M, Santos V, Morais S, Bajouco M, Costa H, Anjo SI, Baldeiras I, Macedo A, Manadas B. Proteomic analysis of peripheral blood mononuclear cells in first episode psychosis - Protein and peptide-centered approaches to elucidate potential diagnostic biomarkers. J Proteomics 2024; 309:105296. [PMID: 39218299 DOI: 10.1016/j.jprot.2024.105296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 08/19/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Diagnosing patients suffering from psychotic disorders is far from being achieved with molecular support, despite all the efforts to study these disorders from different perspectives. Characterizing the proteome of easily obtainable blood specimens, such as the peripheral blood mononuclear cells (PBMCs), has particular interest in biomarker discovery and generating pathophysiological knowledge. This approach has been explored in psychiatry, and while generating valuable information, it has not translated into meaningful biomarker discovery. In this project, we report the proof-of-concept of a methodology that aims to explore further information obtained with classical proteomics approaches that is easily overlooked. PBMC samples from first-episode psychosis and control subjects were subjected to a SWATH-MS approach, and the classical protein relative quantification was performed, where 389 proteins were found to be important to distinguish the two groups. Individual analysis of the quantified peptides was also performed, highlighting peptides of unchanged proteins that were significantly altered. With the combination of protein- and peptide-centered proteomics approaches, it is possible to highlight that information about proteoforms, namely regulation at the peptide level possibly due to post-translational modifications, is routinely overlooked and that its diagnostic potential should be further explored. SIGNIFICANCE: Our exploratory findings highlight the potential of MS-based proteomics strategies, combining protein- and peptide-centered approaches, to aid clinical decision-making in first-episode psychosis, helping to establish early biomarkers for schizophrenia and other psychotic disorders. Particularly, the less popular peptide-centered approach allows the identification/measurement of overlooked modulated peptides that may have potential biomarker characteristics. The application in parallel of protein- and peptide-centered strategies is transversal to research of other diseases, potentially allowing a more comprehensive characterization of the metabolic/pathophysiological alterations related to a specific disease.
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Affiliation(s)
- Catia Santa
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - João E Rodrigues
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Ana Martinho
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Vera M Mendes
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Nuno Madeira
- Faculty of Medicine of the University of Coimbra, University of Coimbra, Portugal; Psychiatry Department, Centro Hospitalar e Universitário de Coimbra, Portugal; CIBIT - Coimbra Institute for Biomedical Imaging and Translational Research, University of Coimbra, Portugal
| | - Manuel Coroa
- CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal; Faculty of Medicine of the University of Coimbra, University of Coimbra, Portugal; Psychiatry Department, Centro Hospitalar e Universitário de Coimbra, Portugal
| | - Vítor Santos
- CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal; Faculty of Medicine of the University of Coimbra, University of Coimbra, Portugal; Psychiatry Department, Centro Hospitalar e Universitário de Coimbra, Portugal
| | - Sofia Morais
- Faculty of Medicine of the University of Coimbra, University of Coimbra, Portugal; Psychiatry Department, Centro Hospitalar e Universitário de Coimbra, Portugal; CIBIT - Coimbra Institute for Biomedical Imaging and Translational Research, University of Coimbra, Portugal
| | - Miguel Bajouco
- Faculty of Medicine of the University of Coimbra, University of Coimbra, Portugal; Psychiatry Department, Centro Hospitalar e Universitário de Coimbra, Portugal; CIBIT - Coimbra Institute for Biomedical Imaging and Translational Research, University of Coimbra, Portugal
| | - Hélder Costa
- Psychiatry Department, Centro Hospitalar e Universitário de Coimbra, Portugal
| | - Sandra I Anjo
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Inês Baldeiras
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal; Faculty of Medicine of the University of Coimbra, University of Coimbra, Portugal
| | - Antonio Macedo
- Faculty of Medicine of the University of Coimbra, University of Coimbra, Portugal; Psychiatry Department, Centro Hospitalar e Universitário de Coimbra, Portugal; CIBIT - Coimbra Institute for Biomedical Imaging and Translational Research, University of Coimbra, Portugal.
| | - Bruno Manadas
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal; III Institute for Interdisciplinary Research, University of Coimbra (IIIUC), Portugal.
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2
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Martins EAG, Deus IA, Gomes MC, Silva AS, Mano JF, Custódio CA. Human Chorionic Membrane-derived Tunable Hydrogels for Vascular Tissue Engineering Strategies. Adv Healthc Mater 2024:e2401510. [PMID: 39101324 DOI: 10.1002/adhm.202401510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 07/17/2024] [Indexed: 08/06/2024]
Abstract
One of the foremost targets in the advancement of biomaterials to engineer vascularized tissues is not only to replicate the composition of the intended tissue but also to create thicker structures incorporating a vascular network for adequate nutrients and oxygen supply. For the first time, to the best of current knowledge, a clinically relevant biomaterial is developed, demonstrating that hydrogels made from the human decellularized extracellular matrix can exhibit robust mechanical properties (in the kPa range) and angiogenic capabilities simultaneously. These properties enable the culture and organization of human umbilical vein endothelial cells into tubular structures, maintaining their integrity for 14 days in vitro without the need for additional polymers or angiogenesis-related factors. This is achieved by repurposing the placenta chorionic membrane (CM), a medical waste with an exceptional biochemical composition, into a valuable resource for bioengineering purposes. After decellularization, the CM underwent chemical modification with methacryloyl groups, giving rise to methacrylated CM (CMMA). CMMA preserved key proteins, as well as glycosaminoglycans. The resulting hydrogels rapidly photopolymerize and have enhanced strength and customizable mechanical properties. Furthermore, they demonstrate angio-vasculogenic competence in vitro and in vivo, holding significant promise as a humanized platform for the engineering of vascularized tissues.
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Affiliation(s)
- Elisa A G Martins
- Department of Chemistry, CICECO, University of Aveiro, Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - Inês A Deus
- Department of Chemistry, CICECO, University of Aveiro, Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - Maria C Gomes
- Department of Chemistry, CICECO, University of Aveiro, Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - Ana S Silva
- Department of Chemistry, CICECO, University of Aveiro, Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - João F Mano
- Department of Chemistry, CICECO, University of Aveiro, Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - Catarina A Custódio
- Department of Chemistry, CICECO, University of Aveiro, Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
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3
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Sousa JPM, Deus IA, Monteiro CF, Custódio CA, Gil J, Papadimitriou L, Ranella A, Stratakis E, Mano JF, Marques PAAP. Amniotic Membrane-Derived Multichannel Hydrogels for Neural Tissue Repair. Adv Healthc Mater 2024:e2400522. [PMID: 38989725 DOI: 10.1002/adhm.202400522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 06/27/2024] [Indexed: 07/12/2024]
Abstract
In the pursuit of advancing neural tissue regeneration, biomaterial scaffolds have emerged as promising candidates, offering potential solutions for nerve disruptions. Among these scaffolds, multichannel hydrogels, characterized by meticulously designed micrometer-scale channels, stand out as instrumental tools for guiding axonal growth and facilitating cellular interactions. This study explores the innovative application of human amniotic membranes modified with methacryloyl domains (AMMA) in neural stem cell (NSC) culture. AMMA hydrogels, possessing a tailored softness resembling the physiological environment, are prepared in the format of multichannel scaffolds to simulate native-like microarchitecture of nerve tracts. Preliminary experiments on AMMA hydrogel films showcase their potential for neural applications, demonstrating robust adhesion, proliferation, and differentiation of NSCs without the need for additional coatings. Transitioning into the 3D realm, the multichannel architecture fosters intricate neuronal networks guiding neurite extension longitudinally. Furthermore, the presence of synaptic vesicles within the cellular arrays suggests the establishment of functional synaptic connections, underscoring the physiological relevance of the developed neuronal networks. This work contributes to the ongoing efforts to find ethical, clinically translatable, and functionally relevant approaches for regenerative neuroscience.
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Affiliation(s)
- Joana P M Sousa
- TEMA - Centre for Mechanical Technology and Automation, Department of Mechanical Engineering, University of Aveiro, Aveiro, 3810-193, Portugal
- CICECO - Department of Chemistry, University of Aveiro, Campus Universitario de Santiago, Aveiro, 3810-193, Portugal
| | - Inês A Deus
- CICECO - Department of Chemistry, University of Aveiro, Campus Universitario de Santiago, Aveiro, 3810-193, Portugal
| | - Cátia F Monteiro
- CICECO - Department of Chemistry, University of Aveiro, Campus Universitario de Santiago, Aveiro, 3810-193, Portugal
| | - Catarina A Custódio
- CICECO - Department of Chemistry, University of Aveiro, Campus Universitario de Santiago, Aveiro, 3810-193, Portugal
- Metatissue, PCI · Creative Science Park Aveiro Region, Via do Conhecimento, Ílhavo, 3830-352, Portugal
| | - João Gil
- TEMA - Centre for Mechanical Technology and Automation, Department of Mechanical Engineering, University of Aveiro, Aveiro, 3810-193, Portugal
- CDRSP - Centre for Rapid and Sustainable Product Development, Polytechnic of Leiria, Marinha Grande, 2430-028, Portugal
- INESC-MN - INESC Microsistemas e Nanotecnologia, Rua Alves Redol 9, Lisbon, 1000-029, Portugal
| | - Lina Papadimitriou
- Institute of Electronic Structure and Laser, Foundation for Research and Technology-Hellas (FORTH-IESL), Heraklion, Greece
| | - Anthi Ranella
- Institute of Electronic Structure and Laser, Foundation for Research and Technology-Hellas (FORTH-IESL), Heraklion, Greece
| | - Emmanuel Stratakis
- Institute of Electronic Structure and Laser, Foundation for Research and Technology-Hellas (FORTH-IESL), Heraklion, Greece
| | - João F Mano
- CDRSP - Centre for Rapid and Sustainable Product Development, Polytechnic of Leiria, Marinha Grande, 2430-028, Portugal
| | - Paula A A P Marques
- TEMA - Centre for Mechanical Technology and Automation, Department of Mechanical Engineering, University of Aveiro, Aveiro, 3810-193, Portugal
- LASI - Intelligent Systems Associate Laboratory, Portugal
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Nickerson JL, Gagnon H, Wentzell PD, Doucette AA. Assessing the precision of a detergent-assisted cartridge precipitation workflow for non-targeted quantitative proteomics. Proteomics 2024; 24:e2300339. [PMID: 38299459 DOI: 10.1002/pmic.202300339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 01/08/2024] [Accepted: 01/12/2024] [Indexed: 02/02/2024]
Abstract
Detergent-based workflows incorporating sodium dodecyl sulfate (SDS) necessitate additional steps for detergent removal ahead of mass spectrometry (MS). These steps may lead to variable protein recovery, inconsistent enzyme digestion efficiency, and unreliable MS signals. To validate a detergent-based workflow for quantitative proteomics, we herein evaluate the precision of a bottom-up sample preparation strategy incorporating cartridge-based protein precipitation with organic solvent to deplete SDS. The variance of data-independent acquisition (SWATH-MS) data was isolated from sample preparation error by modelling the variance as a function of peptide signal intensity. Our SDS-assisted cartridge workflow yield a coefficient of variance (CV) of 13%-14%. By comparison, conventional (detergent-free) in-solution digestion increased the CV to 50%; in-gel digestion provided lower CVs between 14% and 20%. By filtering peptides predicting to display lower precision, we further enhance the validity of data in global comparative proteomics. These results demonstrate the detergent-based precipitation workflow is a reliable approach for in depth, label-free quantitative proteome analysis.
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Affiliation(s)
| | - Hugo Gagnon
- PhenoSwitch Bioscience Inc., Sherbrooke, Quebec, Canada
| | - Peter D Wentzell
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Alan A Doucette
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
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5
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Coelho M, Capela J, Mendes VM, Pacheco J, Fernandes MS, Amendoeira I, Jones JG, Raposo L, Manadas B. Peptidomics Unveils Distinct Acetylation Patterns of Histone and Annexin A1 in Differentiated Thyroid Cancer. Int J Mol Sci 2023; 25:376. [PMID: 38203548 PMCID: PMC10778789 DOI: 10.3390/ijms25010376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/21/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
Thyroid cancer is a common malignancy of the endocrine system. Nodules are routinely evaluated for malignancy risk by fine needle aspiration biopsy (FNAB), and in cases such as follicular lesions, differential diagnosis between benign and malignant nodules is highly uncertain. Therefore, the discovery of new biomarkers for this disease could be helpful in improving diagnostic accuracy. Thyroid nodule biopsies were subjected to a precipitation step with both the insoluble and supernatant fractions subjected to proteome and peptidome profiling. Proteomic analysis identified annexin A1 as a potential biomarker of thyroid cancer malignancy, with its levels increased in malignant samples. Also upregulated were the acetylated peptides of annexin A1, revealed by the peptidome analysis of the supernatant fraction. In addition, supernatant peptidomic analysis revealed a number of acetylated histone peptides that were significantly elevated in the malignant group, suggesting higher gene transcription activity in malignant tissue. Two of these peptides were found to be robust malignancy predictors, with an area under the receiver operating a characteristic curve (ROC AUC) above 0.95. Thus, this combination of proteomics and peptidomics analyses improved the detection of malignant lesions and also provided new evidence linking thyroid cancer development to heightened transcription activity. This study demonstrates the importance of peptidomic profiling in complementing traditional proteomics approaches.
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Affiliation(s)
- Margarida Coelho
- CNC—Center for Neurosciences and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; (M.C.)
- CIBB—Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal
- III Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3030-789 Coimbra, Portugal
- Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
| | - João Capela
- Centro Hospitalar Universitário São João, 4200-319 Porto, Portugal
| | - Vera M. Mendes
- CNC—Center for Neurosciences and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; (M.C.)
- CIBB—Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal
- III Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3030-789 Coimbra, Portugal
| | - João Pacheco
- Centro Hospitalar Universitário São João, 4200-319 Porto, Portugal
| | | | - Isabel Amendoeira
- Centro Hospitalar Universitário São João, 4200-319 Porto, Portugal
- I3S, Instituto de Investigação e Inovação em Saúde, 4200-135 Porto, Portugal
- Ipatimup, Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4200-465 Porto, Portugal
| | - John G. Jones
- CNC—Center for Neurosciences and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; (M.C.)
- CIBB—Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal
- III Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3030-789 Coimbra, Portugal
| | - Luís Raposo
- Portuguese Society of Endocrinology, Diabetes and Metabolism, 1600-892 Lisbon, Portugal
- EPIUnit, Institute of Public Health, University of Porto, 4050-600 Porto, Portugal
| | - Bruno Manadas
- CNC—Center for Neurosciences and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; (M.C.)
- CIBB—Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal
- III Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3030-789 Coimbra, Portugal
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Santa C, Rodrigues D, Coelho JF, Anjo SI, Mendes VM, Bessa-Neto D, Dunn MJ, Cotter D, Baltazar G, Monteiro P, Manadas B. Chronic treatment with D2-antagonist haloperidol leads to inhibitory/excitatory imbalance in striatal D1-neurons. Transl Psychiatry 2023; 13:312. [PMID: 37803004 PMCID: PMC10558446 DOI: 10.1038/s41398-023-02609-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 10/08/2023] Open
Abstract
Striatal dysfunction has been implicated in the pathophysiology of schizophrenia, a disorder characterized by positive symptoms such as hallucinations and delusions. Haloperidol is a typical antipsychotic medication used in the treatment of schizophrenia that is known to antagonize dopamine D2 receptors, which are abundantly expressed in the striatum. However, haloperidol's delayed therapeutic effect also suggests a mechanism of action that may go beyond the acute blocking of D2 receptors. Here, we performed proteomic analysis of striatum brain tissue and found more than 400 proteins significantly altered after 30 days of chronic haloperidol treatment in mice, namely proteins involved in glutamatergic and GABAergic synaptic transmission. Cell-type specific electrophysiological recordings further revealed that haloperidol not only reduces the excitability of striatal medium spiny neurons expressing dopamine D2 receptors (D2-MSNs) but also affects D1-MSNs by increasing the ratio of inhibitory/excitatory synaptic transmission (I/E ratio) specifically onto D1-MSNs but not D2-MSNs. Therefore, we propose the slow remodeling of D1-MSNs as a mechanism mediating the delayed therapeutic effect of haloperidol over striatum circuits. Understanding how haloperidol exactly contributes to treating schizophrenia symptoms may help to improve therapeutic outcomes and elucidate the molecular underpinnings of this disorder.
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Affiliation(s)
- Cátia Santa
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal
- III - Institute of Interdisciplinary Research, University of Coimbra, 3030-789, Coimbra, Portugal
| | - Diana Rodrigues
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Braga/Guimaraes, Portugal
| | - Joana F Coelho
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal
- Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Sandra I Anjo
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal
| | - Vera M Mendes
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal
| | - Diogo Bessa-Neto
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - Michael J Dunn
- Proteome Research Centre, UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine, and Medical Sciences, University College Dublin, Dublin, Ireland
| | - David Cotter
- RCSI Psychiatry, Royal College of Surgeons in Ireland, Education and Research Centre Beaumont, Dublin, Ireland
| | - Graça Baltazar
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - Patrícia Monteiro
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.
- ICVS/3B's-PT Government Associate Laboratory, Braga/Guimaraes, Portugal.
- Department of Biomedicine, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal.
| | - Bruno Manadas
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal.
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Pacheco RI, Cristo MI, Anjo SI, Silva AF, Sousa MI, Tavares RS, Sousa AP, Almeida Santos T, Moura-Ramos M, Caramelo F, Manadas B, Ramalho-Santos J, Amaral SG. New Insights on Sperm Function in Male Infertility of Unknown Origin: A Multimodal Approach. Biomolecules 2023; 13:1462. [PMID: 37892144 PMCID: PMC10605211 DOI: 10.3390/biom13101462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/21/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
The global trend of rising (male) infertility is concerning, and the unidentifiable causes in half of the cases, the so-called unknown origin male infertility (UOMI), demands a better understanding and assessment of both external/internal factors and mechanisms potentially involved. In this work, it was our aim to obtain new insight on UOMI, specifically on idiopathic (ID) and Unexplained male infertility (UMI), relying on a detailed evaluation of the male gamete, including functional, metabolic and proteomic aspects. For this purpose, 1114 semen samples, from males in couples seeking infertility treatment, were collected at the Reproductive Medicine Unit from the Centro Hospitalar e Universitário de Coimbra (CHUC), from July 2018-July 2022. Based on the couples' clinical data, seminal/hormonal analysis, and strict eligibility criteria, samples were categorized in 3 groups, control (CTRL), ID and UMI. Lifestyle factors and anxiety/depression symptoms were assessed via survey. Sperm samples were evaluated functionally, mitochondrially and using proteomics. The results of Assisted Reproduction Techniques were assessed whenever available. According to our results, ID patients presented the worst sperm functional profile, while UMI patients were similar to controls. The proteomic analysis revealed 145 differentially expressed proteins, 8 of which were specifically altered in ID and UMI samples. Acrosin (ACRO) and sperm acrosome membrane-associated protein 4 (SACA4) were downregulated in ID patients while laminin subunit beta-2 (LAMB2), mannose 6-phosphate isomerase (MPI), ATP-dependent 6-phosphofructokinase liver type (PFKAL), STAR domain-containing protein 10 (STA10), serotransferrin (TRFE) and exportin-2 (XPO2) were downregulated in UMI patients. Using random forest analysis, SACA4 and LAMB2 were identified as the sperm proteins with a higher chance of distinguishing ID and UMI patients, and their function and expression variation were in accordance with the functional results. No alterations were observed in terms of lifestyle and psychological factors among the 3 groups. These findings obtained in an experimental setting based on 3 well-defined groups of subjects, might help to validate new biomarkers for unknown origin male infertility (ID and UMI) that, in the future, can be used to improve diagnostics and treatments.
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Affiliation(s)
- Rita I. Pacheco
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Maria I. Cristo
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
- IIIUC—Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Sandra I. Anjo
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
- IIIUC—Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Andreia F. Silva
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
- IIIUC—Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Maria Inês Sousa
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
- Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Renata S. Tavares
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
- Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Ana Paula Sousa
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
- Reproductive Medicine Unit, Centro Hospitalar e Universitário de Coimbra, 3000-075 Coimbra, Portugal
- Eugin Coimbra, Rua Filipe Hodart 12, 3000-185 Coimbra, Portugal
| | - Teresa Almeida Santos
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
- Reproductive Medicine Unit, Centro Hospitalar e Universitário de Coimbra, 3000-075 Coimbra, Portugal
- Eugin Coimbra, Rua Filipe Hodart 12, 3000-185 Coimbra, Portugal
- Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Mariana Moura-Ramos
- Reproductive Medicine Unit, Centro Hospitalar e Universitário de Coimbra, 3000-075 Coimbra, Portugal
- Eugin Coimbra, Rua Filipe Hodart 12, 3000-185 Coimbra, Portugal
- Center for Research in Neuropsychology and Cognitive and Behavioral Intervention, Faculty of Psychology and Educational Sciences, University of Coimbra, 3000-115 Coimbra, Portugal
- Clinical Psychology Unit, Centro Hospitalar e Universitário de Coimbra, 3000-075 Coimbra, Portugal
| | | | - Bruno Manadas
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
- IIIUC—Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - João Ramalho-Santos
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
- Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Sandra Gomes Amaral
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
- IIIUC—Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
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8
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Coelho M, Capela J, Anjo SI, Pacheco J, Fernandes MS, Amendoeira I, Jones JG, Raposo L, Manadas B. Proteomics Reveals mRNA Regulation and the Action of Annexins in Thyroid Cancer. Int J Mol Sci 2023; 24:14542. [PMID: 37833989 PMCID: PMC10572572 DOI: 10.3390/ijms241914542] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
Differentiated thyroid cancer is the most common malignancy of the endocrine system. Although most thyroid nodules are benign, given the high incidence of thyroid nodules in the population, it is important to understand the differences between benign and malignant thyroid cancer and the molecular alterations associated with malignancy to improve detection and signal potential diagnostic, prognostic, and therapeutic targets. Proteomics analysis of benign and malignant human thyroid tissue largely revealed changes indicating modifications in RNA regulation, a common cancer characteristic. In addition, changes in the immune system and cell membrane/endocytic processes were also suggested to be involved. Annexin A1 was considered a potential malignancy biomarker and, similarly to other annexins, it was found to increase in the malignant group. Furthermore, a bioinformatics approach points to the transcription factor Sp1 as being potentially involved in most of the alterations seen in the malignant thyroid nodules.
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Affiliation(s)
- Margarida Coelho
- CNC—Center for Neurosciences and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal; (M.C.)
- CIBB—Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-517 Coimbra, Portugal
- III Institute for Interdisciplinary Research, University of Coimbra (IIIUC), 3030-789 Coimbra, Portugal
- Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
| | - João Capela
- Centro Hospitalar Universitário São João, 4200-319 Porto, Portugal
| | - Sandra I. Anjo
- CNC—Center for Neurosciences and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal; (M.C.)
- CIBB—Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-517 Coimbra, Portugal
- III Institute for Interdisciplinary Research, University of Coimbra (IIIUC), 3030-789 Coimbra, Portugal
| | - João Pacheco
- Centro Hospitalar Universitário São João, 4200-319 Porto, Portugal
| | | | - Isabel Amendoeira
- Centro Hospitalar Universitário São João, 4200-319 Porto, Portugal
- I3S, Instituto de Investigação e Inovação em Saúde, 4200-135 Porto, Portugal
- Ipatimup, Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4200-465 Porto, Portugal
| | - John G. Jones
- CNC—Center for Neurosciences and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal; (M.C.)
- CIBB—Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-517 Coimbra, Portugal
- III Institute for Interdisciplinary Research, University of Coimbra (IIIUC), 3030-789 Coimbra, Portugal
| | - Luís Raposo
- Portuguese Society of Endocrinology, Diabetes and Metabolism, 1600-892 Lisbon, Portugal
- EPIUnit-Institute of Public Health, University of Porto, 4050-600 Porto, Portugal
| | - Bruno Manadas
- CNC—Center for Neurosciences and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal; (M.C.)
- CIBB—Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-517 Coimbra, Portugal
- III Institute for Interdisciplinary Research, University of Coimbra (IIIUC), 3030-789 Coimbra, Portugal
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9
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Pereira C, Castander-Olarieta A, Montalbán IA, Mendes VM, Correia S, Pedrosa A, Manadas B, Moncaleán P, Canhoto J. Proteomic and Metabolic Analysis of Pinus halepensis Mill. Embryonal Masses Induced under Heat Stress. Int J Mol Sci 2023; 24:ijms24087211. [PMID: 37108380 PMCID: PMC10139065 DOI: 10.3390/ijms24087211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/04/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Understanding the physiological and molecular adjustments occurring during tree stress response is of great importance for forest management and breeding programs. Somatic embryogenesis has been used as a model system to analyze various processes occurring during embryo development, including stress response mechanisms. In addition, "priming" plants with heat stress during somatic embryogenesis seems to favor the acquisition of plant resilience to extreme temperature conditions. In this sense, Pinus halepensis somatic embryogenesis was induced under different heat stress treatments (40 °C for 4 h, 50 °C for 30 min, and 60 °C for 5 min) and its effects on the proteome and the relative concentration of soluble sugars, sugar alcohols and amino acids of the embryonal masses obtained were assessed. Heat severely affected the production of proteins, and 27 proteins related to heat stress response were identified; the majority of the proteins with increased amounts in embryonal masses induced at higher temperatures consisted of enzymes involved in the regulation of metabolism (glycolysis, the tricarboxylic acid cycle, amino acid biosynthesis and flavonoids formation), DNA binding, cell division, transcription regulation and the life-cycle of proteins. Finally, significant differences in the concentrations of sucrose and amino acids, such as glutamine, glycine and cysteine, were found.
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Affiliation(s)
- Cátia Pereira
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | | | | | - Vera M Mendes
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Sandra Correia
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- InnovPlantProtect CoLAb, Estrada de Gil Vaz, 7350-478 Elvas, Portugal
| | - Ana Pedrosa
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Bruno Manadas
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Paloma Moncaleán
- Department of Forestry Science, NEIKER-BRTA, 01192 Arkaute, Spain
| | - Jorge Canhoto
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
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10
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Pinto L, Macedo J, Araújo B, Anjo S, Silveira-Rosa T, Patrício P, Teixeira F, Manadas B, Rodrigues AJ, Lepore A, Salgado A, Gomes E. Glial-Restricted Precursors stimulate endogenous cytogenesis and effectively recover emotional deficits in a model of cytogenesis ablation. RESEARCH SQUARE 2023:rs.3.rs-2747462. [PMID: 37034743 PMCID: PMC10081440 DOI: 10.21203/rs.3.rs-2747462/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Adult cytogenesis, the continuous generation of newly-born neurons (neurogenesis) and glial cells (gliogenesis) throughout life, is highly impaired in several neuropsychiatric disorders, such as Major Depressive Disorder (MDD), impacting negatively on cognitive and emotional domains. Despite playing a critical role in brain homeostasis, the importance of gliogenesis has been overlooked, both in healthy and diseased states. To examine the role of newly formed glia, we transplanted Glial Restricted Precursors (GRPs) into the adult hippocampal dentate gyrus (DG), or injected their secreted factors (secretome), into a previously validated transgenic GFAP-tk rat line, in which cytogenesis is transiently compromised. We explored the long-term effects of both treatments on physiological and behavioral outcomes. Grafted GRPs reversed anxiety-like and depressive-like deficits, while the secretome promoted recovery of only anxiety-like behavior. Furthermore, GRPs elicited a recovery of neurogenic and gliogenic levels in the ventral DG, highlighting the unique involvement of these cells in the regulation of brain cytogenesis. Both GRPs and their secretome induced significant alterations in the DG proteome, directly influencing proteins and pathways related to cytogenesis, regulation of neural plasticity and neuronal development. With this work, we demonstrate a valuable and specific contribution of glial progenitors to normalizing gliogenic levels, rescueing neurogenesis and, importantly, promoting recovery of emotional deficits characteristic of disorders such as MDD.
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Affiliation(s)
| | | | | | - Sandra Anjo
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra
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11
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Marote A, Santos D, Mendes-Pinheiro B, Serre-Miranda C, Anjo SI, Vieira J, Ferreira-Antunes F, Correia JS, Borges-Pereira C, Pinho AG, Campos J, Manadas B, Teixeira MR, Correia-Neves M, Pinto L, Costa PM, Roybon L, Salgado AJ. Cellular Aging Secretes: a Comparison of Bone-Marrow-Derived and Induced Mesenchymal Stem Cells and Their Secretome Over Long-Term Culture. Stem Cell Rev Rep 2023; 19:248-263. [PMID: 36152233 DOI: 10.1007/s12015-022-10453-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2022] [Indexed: 01/29/2023]
Abstract
Mesenchymal stem cells (MSCs) hold promising therapeutic potential in several clinical applications, mainly due to their paracrine activity. The implementation of future secretome-based therapeutic strategies requires the use of easily accessible MSCs sources that provide high numbers of cells with homogenous characteristics. MSCs obtained from induced pluripotent stem cells (iMSCs) have been put forward as an advantageous alternative to the gold-standard tissue sources, such as bone marrow (BM-MSCs). In this study, we aimed at comparing the secretome of BM-MSCs and iMSCs over long-term culture. For that, we performed a broad characterization of both sources regarding their identity, proteomic secretome analysis, as well as replicative senescence and associated phenotypes, including its effects on MSCs secretome composition and immunomodulatory action. Our results evidence a rejuvenated phenotype of iMSCs, which is translated into a superior proliferative capacity before the induction of replicative senescence. Despite this significant difference between iMSCs and BM-MSCs proliferation, both untargeted and targeted proteomic analysis revealed a similar secretome composition for both sources in pre-senescent and senescent states. These results suggest that shifting from the use of BM-MSCs to a more advantageous source, like iMSCs, may yield similar therapeutic effects as identified over the past years for this gold-standard MSC source.
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Affiliation(s)
- Ana Marote
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057, Braga, Portugal. .,ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal.
| | - Diogo Santos
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Bárbara Mendes-Pinheiro
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Cláudia Serre-Miranda
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Sandra I Anjo
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Multidisciplinary Institute of Ageing (MIA), University of Coimbra, Coimbra, Portugal
| | - Joana Vieira
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal.,Cancer Genetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (HealthResearch Network), Portuguese Oncology Institute of Porto (IPO Porto) / PortoComprehensive Cancer Center, Porto, Portugal
| | - Filipa Ferreira-Antunes
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Joana Sofia Correia
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Caroline Borges-Pereira
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Andreia G Pinho
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Jonas Campos
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Bruno Manadas
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Manuel R Teixeira
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center, Porto, Portugal.,Cancer Genetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (HealthResearch Network), Portuguese Oncology Institute of Porto (IPO Porto) / PortoComprehensive Cancer Center, Porto, Portugal.,School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
| | - Margarida Correia-Neves
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Luísa Pinto
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal.,Behavioral and Molecular Lab (Bn'ML), University of Minho, Braga, Portugal
| | - Pedro M Costa
- Stemmatters, Biotecnologia e Medicina Regenerativa S.A., Guimarães, Portugal
| | - Laurent Roybon
- Stem Cell Laboratory for CNS Disease Modeling, Wallenberg Neuroscience Center, Department of Experimental Medical Science, Lund University, BMC A10, Lund, Sweden.,Strategic Research Area MultiPark, Lund University, Lund, Sweden.,Lund Stem Cell Center, Lund University, Lund, Sweden
| | - António J Salgado
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
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12
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Chronic stress causes striatal disinhibition mediated by SOM-interneurons in male mice. Nat Commun 2022; 13:7355. [PMID: 36446783 PMCID: PMC9709160 DOI: 10.1038/s41467-022-35028-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 11/16/2022] [Indexed: 11/30/2022] Open
Abstract
Chronic stress (CS) is associated with a number of neuropsychiatric disorders, and it may also contribute to or exacerbate motor function. However, the mechanisms by which stress triggers motor symptoms are not fully understood. Here, we report that CS functionally alters dorsomedial striatum (DMS) circuits in male mice, by affecting GABAergic interneuron populations and somatostatin positive (SOM) interneurons in particular. Specifically, we show that CS impairs communication between SOM interneurons and medium spiny neurons, promoting striatal overactivation/disinhibition and increased motor output. Using probabilistic machine learning to analyze animal behavior, we demonstrate that in vivo chemogenetic manipulation of SOM interneurons in DMS modulates motor phenotypes in stressed mice. Altogether, we propose a causal link between dysfunction of striatal SOM interneurons and motor symptoms in models of chronic stress.
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13
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Zafar S, Noor A, Younas N, Shafiq M, Schmitz M, Wurster I, Brockmann K, Gasser T, Zerr I. SWATH Mass Spectrometry-Based CSF Proteome Profile of GBA-Linked Parkinson's Disease Patients. Int J Mol Sci 2022; 23:ijms232214166. [PMID: 36430645 PMCID: PMC9699576 DOI: 10.3390/ijms232214166] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/07/2022] [Accepted: 11/11/2022] [Indexed: 11/18/2022] Open
Abstract
β-glucocerebrosidase (GBA)-associated mutations are a significant risk factor for Parkinson's disease (PD) that aggravate the disease pathology by upregulating the deposition of α-Synuclein (α-Syn). The resultant clinical profile varies for PD patients without GBA mutations. The current study aimed to identify the proteomic targets involved in the pathogenic pathways leading to the differential clinical presentation of GBA-associated PD. CSF samples (n = 32) were obtained from PD patients with GBA mutations (n = 22), PD patients without GBA mutations (n = 7), and healthy controls that were carriers of GBA mutations (n = 3). All samples were subjected to in-gel tryptic digestion followed by the construction of the spectral library and quantitative SWATH-based analysis. CSF α-Syn levels were reduced in both PDIdiopathic and PDGBA cases. Our SWATH-based mass spectrometric analysis detected 363 proteins involved in immune response, stress response, and cell signaling in various groups. Intergroup analysis showed that 52 proteins were significantly up- or downregulated in various groups. Of these 52 targets, 20 proteins were significantly altered in PDGBA cases only while 2 showed different levels in PDIdiopathic patients. Our results show that the levels of several pathologically relevant proteins, including Contactin-1, Selenium-binding protein 1, Adhesion G Protein-Coupled Receptor, and Apolipoprotein E are significantly different among the sporadic and genetic variants of PD and hint at aggravated synaptic damage, oxidative stress, neuronal loss, and aggregation of α-Syn in PDGBA cases.
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Affiliation(s)
- Saima Zafar
- Clinical Department of Neurology, University Medical Center Göttingen and the German Center for Neurodegenerative Diseases (DZNE), Robert-Koch-Straße 40, 37075 Göttingen, Germany
- Biomedical Engineering and Sciences Department, School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Bolan Road, H-12, Islamabad 44000, Pakistan
- Correspondence: ; Tel.: +49-551-39-65398
| | - Aneeqa Noor
- Clinical Department of Neurology, University Medical Center Göttingen and the German Center for Neurodegenerative Diseases (DZNE), Robert-Koch-Straße 40, 37075 Göttingen, Germany
- Biomedical Engineering and Sciences Department, School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Bolan Road, H-12, Islamabad 44000, Pakistan
| | - Neelam Younas
- Clinical Department of Neurology, University Medical Center Göttingen and the German Center for Neurodegenerative Diseases (DZNE), Robert-Koch-Straße 40, 37075 Göttingen, Germany
| | - Mohsin Shafiq
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Matthias Schmitz
- Clinical Department of Neurology, University Medical Center Göttingen and the German Center for Neurodegenerative Diseases (DZNE), Robert-Koch-Straße 40, 37075 Göttingen, Germany
| | - Isabel Wurster
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research, University of Tübingen, Hoppe-Seyler-Str. 3, 72076 Tübingen, Germany
- German Center for Neurodegenerative Disease (DZNE), 72076 Tübingen, Germany
| | - Kathrin Brockmann
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research, University of Tübingen, Hoppe-Seyler-Str. 3, 72076 Tübingen, Germany
- German Center for Neurodegenerative Disease (DZNE), 72076 Tübingen, Germany
| | - Thomas Gasser
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research, University of Tübingen, Hoppe-Seyler-Str. 3, 72076 Tübingen, Germany
- German Center for Neurodegenerative Disease (DZNE), 72076 Tübingen, Germany
| | - Inga Zerr
- Clinical Department of Neurology, University Medical Center Göttingen and the German Center for Neurodegenerative Diseases (DZNE), Robert-Koch-Straße 40, 37075 Göttingen, Germany
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14
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Mass Spectrometry-Based Proteomic and Metabolomic Profiling of Serum Samples for Discovery and Validation of Tuberculosis Diagnostic Biomarker Signature. Int J Mol Sci 2022; 23:ijms232213733. [PMID: 36430211 PMCID: PMC9694769 DOI: 10.3390/ijms232213733] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 10/26/2022] [Accepted: 11/03/2022] [Indexed: 11/11/2022] Open
Abstract
Tuberculosis (TB) is a transmissible disease listed as one of the 10 leading causes of death worldwide (10 million infected in 2019). A swift and precise diagnosis is essential to forestall its transmission, for which the discovery of effective diagnostic biomarkers is crucial. In this study, we aimed to discover molecular biomarkers for the early diagnosis of tuberculosis. Two independent cohorts comprising 29 and 34 subjects were assayed by proteomics, and 49 were included for metabolomic analysis. All subjects were arranged into three experimental groups—healthy controls (controls), latent TB infection (LTBI), and TB patients. LC-MS/MS blood serum protein and metabolite levels were submitted to univariate, multivariate, and ROC analysis. From the 149 proteins quantified in the discovery set, 25 were found to be differentially abundant between controls and TB patients. The AUC, specificity, and sensitivity, determined by ROC statistical analysis of the model composed of four of these proteins considering both proteomic sets, were 0.96, 93%, and 91%, respectively. The five metabolites (9-methyluric acid, indole-3-lactic acid, trans-3-indoleacrylic acid, hexanoylglycine, and N-acetyl-L-leucine) that better discriminate the control and TB patient groups (VIP > 1.75) from a total of 92 metabolites quantified in both ionization modes were submitted to ROC analysis. An AUC = 1 was determined, with all samples being correctly assigned to the respective experimental group. An integrated ROC analysis enrolling one protein and four metabolites was also performed for the common control and TB patients in the proteomic and metabolomic groups. This combined signature correctly assigned the 12 controls and 12 patients used only for prediction (AUC = 1, specificity = 100%, and sensitivity = 100%). This multiomics approach revealed a biomarker signature for tuberculosis diagnosis that could be potentially used for developing a point-of-care diagnosis clinical test.
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15
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Guatelli S, Ferrario C, Bonasoro F, Anjo SI, Manadas B, Candia Carnevali MD, Varela Coelho A, Sugni M. More than a simple epithelial layer: multifunctional role of echinoderm coelomic epithelium. Cell Tissue Res 2022; 390:207-227. [PMID: 36083358 PMCID: PMC9630195 DOI: 10.1007/s00441-022-03678-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 08/23/2022] [Indexed: 11/02/2022]
Abstract
In echinoderms, the coelomic epithelium (CE) is reportedly the source of new circulating cells (coelomocytes) as well as the provider of molecular factors such as immunity-related molecules. However, its overall functions have been scarcely studied in detail. In this work, we used an integrated approach based on both microscopy (light and electron) and proteomic analyses to investigate the arm CE in the starfish Marthasterias glacialis during different physiological conditions (i.e., non-regenerating and/or regenerating). Our results show that CE cells share both ultrastructural and proteomic features with circulating coelomocytes (echinoderm immune cells). Additionally, microscopy and proteomic analyses indicate that CE cells are actively involved in protein synthesis and processing, and membrane trafficking processes such as phagocytosis (particularly of myocytes) and massive secretion phenomena. The latter might provide molecules (e.g., immune factors) and fluids for proper arm growth/regrowth. No stem cell marker was identified and no pre-existing stem cell was observed within the CE. Rather, during regeneration, CE cells undergo dedifferentiation and epithelial-mesenchymal transition to deliver progenitor cells for tissue replacement. Overall, our work underlines that echinoderm CE is not a "simple epithelial lining" and that instead it plays multiple functions which span from immunity-related roles as well as being a source of regeneration-competent cells for arm growth/regrowth.
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Affiliation(s)
- Silvia Guatelli
- Department of Environmental Science and Policy, University of Milan, Via Celoria 26, 20133, Milan, Italy
| | - Cinzia Ferrario
- Department of Environmental Science and Policy, University of Milan, Via Celoria 26, 20133, Milan, Italy
- Center for Complexity & Biosystems, Department of Physics, University of Milan, Via Celoria 16, 20133, Milan, Italy
| | - Francesco Bonasoro
- Department of Environmental Science and Policy, University of Milan, Via Celoria 26, 20133, Milan, Italy
| | - Sandra I Anjo
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Rua Larga, 3004-504, Coimbra, Portugal
| | - Bruno Manadas
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Rua Larga, 3004-504, Coimbra, Portugal
| | | | - Ana Varela Coelho
- ITQB-Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
| | - Michela Sugni
- Department of Environmental Science and Policy, University of Milan, Via Celoria 26, 20133, Milan, Italy.
- Center for Complexity & Biosystems, Department of Physics, University of Milan, Via Celoria 16, 20133, Milan, Italy.
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16
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Bebianno MJ, Mendes VM, O'Donovan S, Carteny CC, Keiter S, Manadas B. Effects of microplastics alone and with adsorbed benzo(a)pyrene on the gills proteome of Scrobicularia plana. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 842:156895. [PMID: 35753444 DOI: 10.1016/j.scitotenv.2022.156895] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/18/2022] [Accepted: 06/19/2022] [Indexed: 06/15/2023]
Abstract
Microplastics (MPs) are globally present in the marine environment, but the biological effects on marine organisms at the molecular and cellular levels remain scarce. Due to their lipophilic nature, MPs can adsorb other contaminants present in the marine environment, which may increase their detrimental effects once ingested by organisms. This study investigates the effects of low-density polyethylene (PE) MPs with and without adsorbed benzo[a]pyrene (BaP) in the gills proteome of the peppery furrow shell clam, Scrobicularia plana. Clams were exposed to PE MPs (11-13 μm; 1 mg L-1) for 14 days. BaP was analyzed in whole clams' soft tissues, and a proteomic approach was applied in the gills using SWATH/DIA analysis. Proteomic responses suggest that virgin MPs cause disturbance by altering cytoskeleton and cell structure, energy metabolism, conformational changes, oxidative stress, fatty acids, DNA binding and, neurotransmission highlighting the potential risk of this type of MPs for the clam health. Conversely, when clam gills were exposed to MPs adsorbed with BaP a higher differentiation of protein expression was observed that besides changes in cytoskeleton and cell structure, oxidative stress, energy metabolism and DNA binding also induce changes in glucose metabolism, RNA binding and apoptosis. These results indicate that the presence of both stressors (MPs and BaP) have a higher toxicological risk to the health of S. plana.
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Affiliation(s)
- M J Bebianno
- Centre for Marine and Environmental Research (CIMA), University of Algarve, Campus de Gambelas, 8000-397 Faro, Portugal.
| | - Vera M Mendes
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Sarit O'Donovan
- Centre for Marine and Environmental Research (CIMA), University of Algarve, Campus de Gambelas, 8000-397 Faro, Portugal
| | - Camila C Carteny
- Systemic Physiological and Ecotoxicological Research, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Stephen Keiter
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Örebro, Sweden
| | - Bruno Manadas
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
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17
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Beatriz M, Vilaça R, Anjo SI, Manadas B, Januário C, Rego AC, Lopes C. Defective mitochondria-lysosomal axis enhances the release of extracellular vesicles containing mitochondrial DNA and proteins in Huntington's disease. JOURNAL OF EXTRACELLULAR BIOLOGY 2022; 1:e65. [PMID: 38939215 PMCID: PMC11080813 DOI: 10.1002/jex2.65] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/21/2022] [Accepted: 09/23/2022] [Indexed: 06/29/2024]
Abstract
Mitochondrial and autophagy dysfunction are mechanisms proposed to be involved in the pathogenesis of several neurodegenerative diseases. Huntington's disease (HD) is a progressive neurodegenerative disorder associated with mutant Huntingtin-induced abnormalities in neuronal mitochondrial dynamics and quality control. Former studies suggest that the removal of defective mitochondria may be compromised in HD. Mitochondrial quality control (MQC) is a complex, well-orchestrated pathway that can be compromised through mitophagy dysregulation or impairment in the mitochondria-lysosomal axis. Another mitochondrial stress response is the generation of mitochondrial-derived vesicles that fuse with the endolysosomal system and form multivesicular bodies that are extruded from cells as extracellular vesicles (EVs). In this work, we aimed to study the presence of mitochondrial components in human EVs and the relation to the dysfunction of both mitochondria and the autophagy pathway. We comprehensively characterized the mitochondrial and autophagy alterations in premanifest and manifest HD carriers and performed a proteomic and genomic EVs profile. We observed that manifest HD patients exhibit mitochondrial and autophagy impairment associated with enhanced EVs release. Furthermore, we detected mitochondrial DNA and proteins in EVs released by HD cells and in neuronal-derived EVs including VDAC-1 and alpha and beta subunits of ATP synthase F1. HD-extracellular vesicles transport higher levels of mitochondrial genetic material in manifest HD patients, suggesting an alternative pathway for the secretion of reactive mitochondrial components. This study provides a novel framework connecting EVs enhanced release of mitochondrial components to mitochondrial and lysosomal dysfunction in HD.
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Affiliation(s)
- Margarida Beatriz
- CNC‐Center for Neuroscience and Cell BiologyCIBB ‐ Centre for Innovative Biomedicine and BiotechnologyUniversity of CoimbraCoimbraPortugal
- IIIUC‐Institute for Interdisciplinary ResearchUniversity of CoimbraCoimbraPortugal
| | - Rita Vilaça
- CNC‐Center for Neuroscience and Cell BiologyCIBB ‐ Centre for Innovative Biomedicine and BiotechnologyUniversity of CoimbraCoimbraPortugal
- IIIUC‐Institute for Interdisciplinary ResearchUniversity of CoimbraCoimbraPortugal
| | - Sandra I. Anjo
- CNC‐Center for Neuroscience and Cell BiologyCIBB ‐ Centre for Innovative Biomedicine and BiotechnologyUniversity of CoimbraCoimbraPortugal
- Multidisciplinary Institute of AgeingUniversity of CoimbraCoimbraPortugal
| | - Bruno Manadas
- CNC‐Center for Neuroscience and Cell BiologyCIBB ‐ Centre for Innovative Biomedicine and BiotechnologyUniversity of CoimbraCoimbraPortugal
| | | | - A. Cristina Rego
- CNC‐Center for Neuroscience and Cell BiologyCIBB ‐ Centre for Innovative Biomedicine and BiotechnologyUniversity of CoimbraCoimbraPortugal
- FMUC‐Faculty of MedicineUniversity of CoimbraCoimbraPortugal
| | - Carla Lopes
- CNC‐Center for Neuroscience and Cell BiologyCIBB ‐ Centre for Innovative Biomedicine and BiotechnologyUniversity of CoimbraCoimbraPortugal
- IIIUC‐Institute for Interdisciplinary ResearchUniversity of CoimbraCoimbraPortugal
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COVID-19 Salivary Protein Profile: Unravelling Molecular Aspects of SARS-CoV-2 Infection. J Clin Med 2022; 11:jcm11195571. [PMID: 36233441 PMCID: PMC9570692 DOI: 10.3390/jcm11195571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 09/16/2022] [Accepted: 09/17/2022] [Indexed: 11/18/2022] Open
Abstract
COVID-19 is the most impacting global pandemic of all time, with over 600 million infected and 6.5 million deaths worldwide, in addition to an unprecedented economic impact. Despite the many advances in scientific knowledge about the disease, much remains to be clarified about the molecular alterations induced by SARS-CoV-2 infection. In this work, we present a hybrid proteomics and in silico interactomics strategy to establish a COVID-19 salivary protein profile. Data are available via ProteomeXchange with identifier PXD036571. The differential proteome was narrowed down by the Partial Least-Squares Discriminant Analysis and enrichment analysis was performed with FunRich. In parallel, OralInt was used to determine interspecies Protein-Protein Interactions between humans and SARS-CoV-2. Five dysregulated biological processes were identified in the COVID-19 proteome profile: Apoptosis, Energy Pathways, Immune Response, Protein Metabolism and Transport. We identified 10 proteins (KLK 11, IMPA2, ANXA7, PLP2, IGLV2-11, IGHV3-43D, IGKV2-24, TMEM165, VSIG10 and PHB2) that had never been associated with SARS-CoV-2 infection, representing new evidence of the impact of COVID-19. Interactomics analysis showed viral influence on the host immune response, mainly through interaction with the degranulation of neutrophils. The virus alters the host’s energy metabolism and interferes with apoptosis mechanisms.
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19
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Trindade F, Ferreira AF, Saraiva F, Martins D, Mendes VM, Sousa C, Gavina C, Leite-Moreira A, Manadas B, Falcão-Pires I, Vitorino R. Optimization of a Protocol for Protein Extraction from Calcified Aortic Valves for Proteomics Applications: Development of a Standard Operating Procedure. Proteomes 2022; 10:proteomes10030030. [PMID: 36136308 PMCID: PMC9505568 DOI: 10.3390/proteomes10030030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/02/2022] [Accepted: 08/11/2022] [Indexed: 11/28/2022] Open
Abstract
The comprehension of the pathophysiological mechanisms, the identification of druggable targets, and putative biomarkers for aortic valve stenosis can be pursued through holistic approaches such as proteomics. However, tissue homogenization and protein extraction are made difficult by tissue calcification. The reproducibility of proteome studies is key in clinical translation of the findings. Thus, we aimed to optimize a protocol for aortic valve homogenization and protein extraction and to develop a standard operating procedure (SOP), which researchers can use to maximize protein yield while reducing inter-laboratory variability. We have compared the protein yield between conventional tissue grinding in nitrogen followed by homogenization with a Potter apparatus with a more advanced bead-beating system. Once we confirmed the superiority of the latter, we further optimized it by testing the effect of beads size, the number of homogenization cycles, tube capacity, lysis buffer/tissue mass ratio, and two different lysis buffers. Optimal protein extraction was achieved with 2.8 mm zirconium dioxide beads, in two homogenization cycles, in the presence of 20 µL RIPA buffer/mg tissue, using 2 mL O-ring cryotubes. As a proof of concept of the usefulness of this SOP for proteomics, the AV proteome of men and women with aortic stenosis was characterized, resulting in the quantification of proteins across six orders of magnitude and uncovering some putative proteins dysregulated by sex.
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Affiliation(s)
- Fábio Trindade
- Cardiovascular R&D Centre—UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- Correspondence:
| | - Ana F. Ferreira
- Cardiovascular R&D Centre—UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - Francisca Saraiva
- Cardiovascular R&D Centre—UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - Diana Martins
- Cardiovascular R&D Centre—UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - Vera M. Mendes
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Carla Sousa
- Cardiovascular R&D Centre—UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- Cardiology Department, Centro Hospitalar Universitário de São João, 4200-319 Porto, Portugal
| | - Cristina Gavina
- Cardiovascular R&D Centre—UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- Cardiology Department, Hospital Pedro Hispano, Unidade Local de Saúde de Matosinhos, 4464-513 Matosinhos, Portugal
| | - Adelino Leite-Moreira
- Cardiovascular R&D Centre—UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- Department of Cardiothoracic Surgery, Centro Hospitalar Universitário de São João, 4200-319 Porto, Portugal
| | - Bruno Manadas
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
- Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Inês Falcão-Pires
- Cardiovascular R&D Centre—UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - Rui Vitorino
- Cardiovascular R&D Centre—UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- iBiMED—Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal
- LAQV/REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
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20
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Castander-Olarieta A, Pereira C, Mendes VM, Correia S, Manadas B, Canhoto J, Montalbán IA, Moncaleán P. Thermopriming-associated proteome and sugar content responses in Pinus radiata embryogenic tissue. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 321:111327. [PMID: 35696927 DOI: 10.1016/j.plantsci.2022.111327] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/02/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Improving the capacity of plants to face adverse environmental conditions requires a deep understanding of the molecular mechanisms governing stress response and adaptation. Proteomics, combined with metabolic analyses, offers a wide resource of information to be used in plant breeding programs. Previous studies have shown that somatic embryogenesis in Pinus spp. is a suitable tool not only to investigate stress response processes but also to modulate the behaviour of somatic plants. Based on this, the objective of this study was to analyse the protein and soluble sugar profiles of Pinus radiata embryonal masses after the application of high temperatures to unravel the mechanisms involved in thermopriming and memory acquisition at early stages of the somatic embryogenesis process. Results confirmed that heat provokes deep readjustments in the life cycle of proteins, together with a significant reduction in the carbon-flux of central-metabolism pathways. Heat-priming also promotes the accumulation of proteins involved in oxidative stress defence, in the synthesis of specific amino acids such as isoleucine, influences cell division, the organization of the cytoskeleton and cell-walls, and modifies the levels of free soluble sugars like glucose or fructose. All this seems to be regulated by proteins linked with epigenetic, transcriptional and post-transcriptional mechanisms.
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Affiliation(s)
| | - Cátia Pereira
- Department of Forestry Science, NEIKER-BRTA, Arkaute, Spain; Center for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Vera M Mendes
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Sandra Correia
- Center for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Bruno Manadas
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Jorge Canhoto
- Center for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
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21
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Proteomics of Fish White Muscle and Western Blotting to Detect Putative Allergens. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2498:397-411. [PMID: 35727560 DOI: 10.1007/978-1-0716-2313-8_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A detailed workflow is provided for preparation from teleost fish white muscle of extracts for proteomics analysis. The protocol generates samples that can be analyzed by SWATH (Sequential Window data independent Acquisition of the Total High-resolution-Mass Spectra), a modern MS-based quantitative label free technology. The main steps for the extraction of three independent protein fractions, (1) soluble sarcoplasmic, (2) soluble myofibrillar, and (3) insoluble material, from fish white muscle are detailed. Coupled to the protein extraction protocol a Western blotting approach is outlined for detection of common fish allergens, in this case β-parvalbumin, in the white muscle sarcoplasmic protein fraction.
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22
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Pinto PI, Anjos L, Estêvão MD, Santos S, Santa C, Manadas B, Monsinjon T, Canário AVM, Power DM. Proteomics of sea bass skin-scales exposed to the emerging pollutant fluoxetine compared to estradiol. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 814:152671. [PMID: 34968595 DOI: 10.1016/j.scitotenv.2021.152671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
Teleost fish skin-scales are essential for protection and homeostasis and the largest tissue in direct contact with the environment, but their potential as early indicators of pollutant exposure are hampered by limited knowledge about this model. This study evaluated multi-level impacts of in vivo exposure of European sea bass to fluoxetine (FLX, a selective serotonin-reuptake inhibitor and an emerging pollutant) and 17β-estradiol (E2, a natural hormone and representative of diverse estrogenic endocrine-disrupting pollutants). Exposed fish had significantly increased circulating levels of FLX and its active metabolite nor-FLX that, in contrast to E2, did not have estrogenic effects on most fish plasma and scale indicators. Quantitative proteomics using SWATH-MS identified 985 proteins in the scale total proteome. 213 proteins were significantly modified 5 days after exposure to E2 or FLX and 31 were common to both treatments and responded in the same way. Common biological processes significantly affected by both treatments were protein turnover and cytoskeleton reorganization. E2 specifically up-regulated proteins related to protein production and degradation and down-regulated the cytoskeleton/extracellular matrix and innate immune proteins. FLX caused both up- and down-regulation of protein synthesis and energy metabolism. Multiple estrogen and serotonin receptor and transporter transcripts were altered in sea bass scales after E2 and/or FLX exposure, revealing complex disruptive effects in estrogen/serotonin responsiveness, which may account for the partially overlapping effects of E2 and FLX on the proteome. A large number (103) of FLX-specifically regulated proteins indicated numerous actions independent of estrogen signalling. This study provides the first quantitative proteome of the fish skin-scale barrier, elucidates routes of action and biochemical and molecular signatures of E2 or FLX-exposure and identifies potential physiological consequences and candidate biomarkers of pollutant exposure, for monitoring and risk assessment.
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Affiliation(s)
- Patricia I Pinto
- CCMAR - Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal.
| | - L Anjos
- CCMAR - Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal
| | - M D Estêvão
- CCMAR - Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal; Escola Superior de Saúde da Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - S Santos
- CCMAR - Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal
| | - C Santa
- CNC - Center for Neuroscience and Cell Biology, Universidade de Coimbra, 3004-517 Coimbra, Portugal; Institute for Interdisciplinary Research (IIIUC), Universidade de Coimbra, 3004-517 Coimbra, Portugal
| | - B Manadas
- CNC - Center for Neuroscience and Cell Biology, Universidade de Coimbra, 3004-517 Coimbra, Portugal; Institute for Interdisciplinary Research (IIIUC), Universidade de Coimbra, 3004-517 Coimbra, Portugal
| | - T Monsinjon
- Normandy University, Environmental Stress and Aquatic Biomonitoring (SEBIO), Université Le Havre Normandie, 76600 Le Havre, France
| | - Adelino V M Canário
- CCMAR - Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal
| | - D M Power
- CCMAR - Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal.
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23
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Anjos L, Pinto PIS, Santos S, Estêvão MD, Santa C, Manadas B, Canário AVM, Power DM. Proteome dataset of sea bass ( Dicentrarchus labrax) skin-scales exposed to fluoxetine and estradiol. Data Brief 2022; 41:107971. [PMID: 35252491 PMCID: PMC8889360 DOI: 10.1016/j.dib.2022.107971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/10/2022] [Accepted: 02/14/2022] [Indexed: 11/17/2022] Open
Abstract
Contamination of aquatic ecosystems with anthropogenic pollutants, including pharmaceutical drugs, is a major concern worldwide. Aquatic organisms such as fish are particularly at risk of exposure to pollutants. The surface of fish is the first point of contact with pollutants, but few studies have considered the impact of pollutants on the skin-scale barrier. The present proteome data are the basis of the findings discussed in the associated research article “Proteomics of sea bass skin-scales exposed to the emerging pollutant fluoxetine compared to estradiol” [1]. Juvenile sea bass were exposed by intraperitoneal injections to: a) the antidepressant fluoxetine (FLX), a widely prescribed psychotropic drug and an emerging pollutant; b) the natural estrogen 17β-estradiol (E2) and c) the vehicle, coconut oil (control). The scale proteome of fish exposed to these compounds for 5 days was analysed using quantitative label-free proteomics technology SWATH-MS (sequential windowed data-independent acquisition of the total high-resolution-mass spectra). The proteome data generated was submitted to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD020983. LC-MS data from pooled protein extracts from the scales of all experimental groups was acquired using information-dependent acquisition (IDA) and 1,254 proteins were identified by searching against the sea bass genome database. 715 proteins were quantified by SWATH acquisition, and 213 proteins had modified levels (p < 0.05) between the E2- or FLX-exposed fish compared to the control. The main biological processes and KEGG pathways affected by E2 or FLX treatments were identified using Cytoscape/ClueGO enrichment analyses.
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Affiliation(s)
- Liliana Anjos
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139, Faro, Portugal
| | - Patrícia I S Pinto
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139, Faro, Portugal
| | - Soraia Santos
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139, Faro, Portugal
| | - M Dulce Estêvão
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139, Faro, Portugal.,Escola Superior de Saúde da Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Cátia Santa
- CNC - Center for Neuroscience and Cell Biology, Universidade de Coimbra, 3004-517, Coimbra, Portugal.,Institute for Interdisciplinary Research (IIIUC), Universidade de Coimbra, 3004-517, Coimbra, Portugal
| | - Bruno Manadas
- CNC - Center for Neuroscience and Cell Biology, Universidade de Coimbra, 3004-517, Coimbra, Portugal.,Institute for Interdisciplinary Research (IIIUC), Universidade de Coimbra, 3004-517, Coimbra, Portugal
| | - Adelino V M Canário
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139, Faro, Portugal.,Shanghai Ocean University International Center for Marine Studies, Shanghai 201306, China
| | - Deborah M Power
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139, Faro, Portugal.,Shanghai Ocean University International Center for Marine Studies, Shanghai 201306, China
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Spotted Fever Group Rickettsia Trigger Species-Specific Alterations in Macrophage Proteome Signatures with Different Impacts in Host Innate Inflammatory Responses. Microbiol Spectr 2021; 9:e0081421. [PMID: 34935429 PMCID: PMC8693926 DOI: 10.1128/spectrum.00814-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The molecular details underlying differences in pathogenicity between Rickettsia species remain to be fully understood. Evidence points to macrophage permissiveness as a key mechanism in rickettsial virulence. Different studies have shown that several rickettsial species responsible for mild forms of rickettsioses can also escape macrophage-mediated killing mechanisms and establish a replicative niche within these cells. However, their manipulative capacity with respect to host cellular processes is far from being understood. A deeper understanding of the interplay between mildly pathogenic rickettsiae and macrophages and the commonalities and specificities of host responses to infection would illuminate differences in immune evasion mechanisms and pathogenicity. We used quantitative proteomics by sequential windowed data independent acquisition of the total high-resolution mass spectra with tandem mass spectrometry (SWATH-MS/MS) to profile alterations resulting from infection of THP-1 macrophages with three mildly pathogenic rickettsiae: Rickettsia parkeri, Rickettsia africae, and Rickettsia massiliae, all successfully proliferating in these cells. We show that all three species trigger different proteome signatures. Our results reveal a significant impact of infection on proteins categorized as type I interferon responses, which here included several components of the retinoic acid-inducible gene I (RIG-1)-like signaling pathway, mRNA splicing, and protein translation. Moreover, significant differences in protein content between infection conditions provide evidence for species-specific induced alterations. Indeed, we confirm distinct impacts on host inflammatory responses between species during infection, demonstrating that these species trigger different levels of beta interferon (IFN-β), differences in the bioavailability of the proinflammatory cytokine interleukin 1β (IL-1β), and differences in triggering of pyroptotic events. This work reveals novel aspects and exciting nuances of macrophage-Rickettsia interactions, adding additional layers of complexity between Rickettsia and host cells' constant arms race for survival. IMPORTANCE The incidence of diseases caused by Rickettsia has been increasing over the years. It has long been known that rickettsioses comprise diseases with a continuous spectrum of severity. There are highly pathogenic species causing diseases that are life threatening if untreated, others causing mild forms of the disease, and a third group for which no pathogenicity to humans has been described. These marked differences likely reflect distinct capacities for manipulation of host cell processes, with macrophage permissiveness emerging as a key virulence trait. However, what defines pathogenicity attributes among rickettsial species is far from being resolved. We demonstrate that the mildly pathogenic Rickettsia parkeri, Rickettsia africae, and Rickettsia massiliae, all successfully proliferating in macrophages, trigger different proteome signatures in these cells and differentially impact critical components of innate immune responses by inducing different levels of beta interferon (IFN-β) and interleukin 1β (IL-1β) and different timing of pyroptotic events during infection. Our work reveals novel nuances in rickettsia-macrophage interactions, offering new clues to understand Rickettsia pathogenicity.
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Chronic pain susceptibility is associated with anhedonic behavior and alterations in the accumbal ubiquitin-proteasome system. Pain 2021; 162:1722-1731. [PMID: 33449505 DOI: 10.1097/j.pain.0000000000002192] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 12/30/2020] [Indexed: 12/18/2022]
Abstract
ABSTRACT It remains unknown why on similar acute/subacute painful conditions, pain persists in some individuals while in others it resolves. Genetic factors, mood, and functional alterations, particularly involving the mesolimbic network, seem to be key. To explore potential susceptibility or resistance factors, we screened a large population of rats with a peripheral neuropathy and we isolated a small subset (<15%) that presented high thresholds (HTs) to mechanical allodynia (reduced pain manifestation). The phenotype was sustained over 12 weeks and was associated with higher hedonic behavior when compared with low-threshold (LT) subjects. The nucleus accumbens of HT and LT animals were isolated for proteomic analysis by Sequential Window Acquisition of All Theoretical Mass Spectra. Two hundred seventy-nine proteins displayed different expression between LT and HT animals or subjects. Among several protein families, the proteasome pathway repeatedly emerged in gene ontology enrichment and KEGG analyses. Several alpha and beta 20S proteasome subunits were increased in LT animals when compared with HT animals (eg, PSMα1, PSMα2, and PSMβ5). On the contrary, UBA6, an upstream ubiquitin-activating enzyme, was decreased in LT animals. Altogether these observations are consistent with an overactivation of the accumbal proteasome pathway in animals that manifest pain and depressive-like behaviors after a neuropathic injury. All the proteomic data are available through ProteomeXchange with identifier PXD022478.
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Bickner AN, Champion MM, Hummon AB, Bruening ML. Electroblotting through a tryptic membrane for LC-MS/MS analysis of proteins separated in electrophoretic gels. Analyst 2021; 145:7724-7735. [PMID: 33000802 DOI: 10.1039/d0an01380c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Digestion of proteins separated via sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) remains a popular method for protein identification using mass-spectrometry based proteomics. Although robust and routine, the in-gel digestion procedure is laborious and time-consuming. Electroblotting to a capture membrane prior to digestion reduces preparation steps but requires on-membrane digestion that yields fewer peptides than in-gel digestion. This paper develops direct electroblotting through a trypsin-containing membrane to a capture membrane to simplify extraction and digestion of proteins separated by SDS-PAGE. Subsequent liquid chromatography-tandem mass spectrometry (LC-MS/MS) identifies the extracted peptides. Analysis of peptides from different capture membrane pieces shows that electrodigestion does not greatly disturb the spatial resolution of a standard protein mixture separated by SDS-PAGE. Electrodigestion of an Escherichia coli (E. coli) cell lysate requires four hours of total sample preparation and results in only 13% fewer protein identifications than in-gel digestion, which can take 24 h. Compared to simple electroblotting and protein digestion on a poly(vinylidene difluoride) (PVDF) capture membrane, adding a trypsin membrane to the electroblot increases the number of protein identifications by 22%. Additionally, electrodigestion experiments using capture membranes coated with polyelectrolyte layers identify a higher fraction of small proteolytic peptides than capture on PVDF or in-gel digestion.
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Affiliation(s)
- A N Bickner
- Department of Chemistry and Biochemistry University of Notre Dame, Notre Dame, Indiana 46556, USA.
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27
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Novais EJ, Choi H, Madhu V, Suyama K, Anjo SI, Manadas B, Shapiro IM, Salgado AJ, Risbud MV. Hypoxia and Hypoxia-Inducible Factor-1α Regulate Endoplasmic Reticulum Stress in Nucleus Pulposus Cells: Implications of Endoplasmic Reticulum Stress for Extracellular Matrix Secretion. THE AMERICAN JOURNAL OF PATHOLOGY 2021; 191:487-502. [PMID: 33307037 PMCID: PMC7927276 DOI: 10.1016/j.ajpath.2020.11.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 11/03/2020] [Accepted: 11/24/2020] [Indexed: 12/20/2022]
Abstract
Endoplasmic reticulum (ER) stress is shown to promote nucleus pulposus (NP) cell apoptosis and intervertebral disc degeneration. However, little is known about ER stress regulation by the hypoxic disc microenvironment and its contribution to extracellular matrix homeostasis. NP cells were cultured under hypoxia (1% partial pressure of oxygen) to assess ER stress status, and gain-of-function and loss-of-function approaches were used to assess the role of hypoxia-inducible factor (HIF)-1α in this pathway. In addition, the contribution of ER stress induction on the NP cell secretome was assessed by a nontargeted quantitative proteomic analysis by sequential windowed data independent acquisition of the total high-resolution mass spectra-mass spectrometry. NP cells exhibited a lower ER stress burden under hypoxia. Knockdown of HIF-1α increased C/EBP homologous protein, protein kinase RNA-like endoplasmic reticulum kinase (PERK), and activating transcription factor 6 (ATF6) levels, whereas HIF-1α stabilization decreased the expression of ER stress markers Ddit3, Hsp5a, Atf6, and Eif2a. Interestingly, ER stress inducers tunicamycin and thapsigargin induced HIF-1α activity under hypoxia while promoting the unfolded protein response. NP cell secretome analysis demonstrated an impact of ER stress induction on extracellular matrix secretion, with decreases in collagens and cell adhesion-related proteins. Moreover, analysis of transcriptomic data of NP tissues from aged mice and degenerated human discs showed higher levels of unfolded protein response markers and decreased levels of matrix components. Our study shows, for the first time, that hypoxia and HIF-1α attenuate ER stress responses in NP cells, and ER stress promotes inefficient extracellular matrix secretion under hypoxia.
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Affiliation(s)
- Emanuel J Novais
- Department of Orthopedic Surgery, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania; Graduate Program in Cell Biology and Regenerative Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania; Life and Health Sciences Research Institute, School of Medicine, University of Minho, Braga, Portugal; Life and Health Sciences Research Institute/Biomaterials, Biodegradables and Biomimetics (ICVS/3B's) - PT Government Associate Laboratory, Braga, Portugal
| | - Hyowon Choi
- Department of Orthopedic Surgery, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania; Graduate Program in Cell Biology and Regenerative Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Vedavathi Madhu
- Department of Orthopedic Surgery, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania; Graduate Program in Cell Biology and Regenerative Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Kaori Suyama
- Department of Orthopedic Surgery, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania; Department of Anatomy and Cellular Biology, Tokai University School of Medicine, Isehara, Japan
| | - Sandra I Anjo
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Bruno Manadas
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Irving M Shapiro
- Department of Orthopedic Surgery, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania; Graduate Program in Cell Biology and Regenerative Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - António J Salgado
- Life and Health Sciences Research Institute, School of Medicine, University of Minho, Braga, Portugal; Life and Health Sciences Research Institute/Biomaterials, Biodegradables and Biomimetics (ICVS/3B's) - PT Government Associate Laboratory, Braga, Portugal
| | - Makarand V Risbud
- Department of Orthopedic Surgery, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania; Graduate Program in Cell Biology and Regenerative Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania.
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Coelho AC, Pires R, Schütz G, Santa C, Manadas B, Pinto P. Disclosing proteins in the leaves of cork oak plants associated with the immune response to Phytophthora cinnamomi inoculation in the roots: A long-term proteomics approach. PLoS One 2021; 16:e0245148. [PMID: 33481834 PMCID: PMC7822296 DOI: 10.1371/journal.pone.0245148] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/22/2020] [Indexed: 02/06/2023] Open
Abstract
The pathological interaction between oak trees and Phytophthora cinnamomi has implications in the cork oak decline observed over the last decades in the Iberian Peninsula. During host colonization, the phytopathogen secretes effector molecules like elicitins to increase disease effectiveness. The objective of this study was to unravel the proteome changes associated with the cork oak immune response triggered by P. cinnamomi inoculation in a long-term assay, through SWATH-MS quantitative proteomics performed in the oak leaves. Using the Arabidopis proteome database as a reference, 424 proteins were confidently quantified in cork oak leaves, of which 80 proteins showed a p-value below 0.05 or a fold-change greater than 2 or less than 0.5 in their levels between inoculated and control samples being considered as altered. The inoculation of cork oak roots with P. cinnamomi increased the levels of proteins associated with protein-DNA complex assembly, lipid oxidation, response to endoplasmic reticulum stress, and pyridine-containing compound metabolic process in the leaves. In opposition, several proteins associated with cellular metabolic compound salvage and monosaccharide catabolic process had significantly decreased abundances. The most significant abundance variations were observed for the Ribulose 1,5-Bisphosphate Carboxylase small subunit (RBCS1A), Heat Shock protein 90–1 (Hsp90-1), Lipoxygenase 2 (LOX2) and Histone superfamily protein H3.3 (A8MRLO/At4G40030) revealing a pertinent role for these proteins in the host-pathogen interaction mechanism. This work represents the first SWATH-MS analysis performed in cork oak plants inoculated with P. cinnamomi and highlights host proteins that have a relevant action in the homeostatic states that emerge from the interaction between the oomycete and the host in the long term and in a distal organ.
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Affiliation(s)
- Ana Cristina Coelho
- Center for Electronic, Optoelectronic and Telecommunications (CEOT), University of Algarve, Faro, Portugal
- Escola Superior de Educação e Comunicação (ESEC), University of Algarve, Faro, Portugal
- * E-mail:
| | - Rosa Pires
- Center for Electronic, Optoelectronic and Telecommunications (CEOT), University of Algarve, Faro, Portugal
| | - Gabriela Schütz
- Center for Electronic, Optoelectronic and Telecommunications (CEOT), University of Algarve, Faro, Portugal
- Instituto Superior de Engenharia, University of Algarve, Faro, Portugal
| | - Cátia Santa
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Coimbra, Portugal
| | - Bruno Manadas
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Patrícia Pinto
- Center for Marine Sciences (CCMAR), University of Algarve, Faro, Portugal
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Cardoso JMS, Anjo SI, Manadas B, Silva H, Abrantes I, Nakamura K, Fonseca L. Virulence Biomarkers of Bursaphelenchus xylophilus: A Proteomic Approach. FRONTIERS IN PLANT SCIENCE 2021; 12:822289. [PMID: 35211137 PMCID: PMC8861294 DOI: 10.3389/fpls.2021.822289] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/28/2021] [Indexed: 05/19/2023]
Abstract
The pinewood nematode (PWN), Bursaphelenchus xylophilus, one of the most serious forest pests worldwide, is considered the causal agent of the pine wilt disease (PWD). The main host species belong to the genus Pinus, and a variation in the susceptibility of several pine species to PWN infection is well-known. It is also recognized that there is variation in the virulence among B. xylophilus isolates. In the present study, we applied a quantitative mass spectrometry-based proteomics approach to perform a deep characterization of proteomic changes across two B. xylophilus isolates with different virulence from different hosts and geographical origins. A total of 1,456 proteins were quantified and compared in the two isolates secretomes, and a total of 2,741 proteins were quantified and compared in the nematode proteomes in pine tree extract and fungus stimuli conditions. From the proteomic analyses, a group of proteins was selected and identified as potential virulence biomarkers and shed light on putative most pathogenic proteins of this plant-parasitic nematode. Proteomic data are available via ProteomeXchange with identifier PXD029377.
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Affiliation(s)
- Joana M. S. Cardoso
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal
- *Correspondence: Joana M. S. Cardoso,
| | - Sandra I. Anjo
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Bruno Manadas
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Hugo Silva
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal
| | - Isabel Abrantes
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal
| | - Katsunori Nakamura
- Tohoku Research Center, Forestry and Forest Products Research Institute, Morioka, Japan
| | - Luís Fonseca
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal
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30
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Castander-Olarieta A, Pereira C, Montalbán IA, Mendes VM, Correia S, Suárez-Álvarez S, Manadas B, Canhoto J, Moncaleán P. Proteome-Wide Analysis of Heat-Stress in Pinus radiata Somatic Embryos Reveals a Combined Response of Sugar Metabolism and Translational Regulation Mechanisms. FRONTIERS IN PLANT SCIENCE 2021; 12:631239. [PMID: 33912202 PMCID: PMC8072280 DOI: 10.3389/fpls.2021.631239] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/22/2021] [Indexed: 05/06/2023]
Abstract
Somatic embryogenesis is the process by which bipolar structures with no vascular connection with the surrounding tissue are formed from a single or a group of vegetative cells, and in conifers it can be divided into five different steps: initiation, proliferation, maturation, germination and acclimatization. Somatic embryogenesis has long been used as a model to study the mechanisms regulating stress response in plants, and recent research carried out in our laboratory has demonstrated that high temperatures during initial stages of conifer somatic embryogenesis modify subsequent phases of the process, as well as the behavior of the resulting plants ex vitro. The development of high-throughput techniques has facilitated the study of the molecular response of plants to numerous stress factors. Proteomics offers a reliable image of the cell status and is known to be extremely susceptible to environmental changes. In this study, the proteome of radiata pine somatic embryos was analyzed by LC-MS after the application of high temperatures during initiation of embryonal masses [(23°C, control; 40°C (4 h); 60°C (5 min)]. At the same time, the content of specific soluble sugars and sugar alcohols was analyzed by HPLC. Results confirmed a significant decrease in the initiation rate of embryonal masses under 40°C treatments (from 44 to 30.5%) and an increasing tendency in the production of somatic embryos (from 121.87 to 170.83 somatic embryos per gram of embryogenic tissue). Besides, heat provoked a long-term readjustment of the protein synthesis machinery: a great number of structural constituents of ribosomes were increased under high temperatures, together with the down-regulation of the enzyme methionine-tRNA ligase. Heat led to higher contents of heat shock proteins and chaperones, transmembrane transport proteins, proteins related with post-transcriptional regulation (ARGONAUTE 1D) and enzymes involved in the synthesis of fatty acids, specific compatible sugars (myo-inositol) and cell-wall carbohydrates. On the other hand, the protein adenosylhomocysteinase and enzymes linked with the glycolytic pathway, nitrogen assimilation and oxidative stress response were found at lower levels.
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Affiliation(s)
| | - Cátia Pereira
- Department of Forestry Science, NEIKER, Arkaute, Spain
- Center for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | | | - Vera M. Mendes
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Sandra Correia
- Center for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | | | - Bruno Manadas
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Jorge Canhoto
- Center for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Paloma Moncaleán
- Department of Forestry Science, NEIKER, Arkaute, Spain
- *Correspondence: Paloma Moncaleán,
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Silva H, Anjo SI, Manadas B, Abrantes I, Fonseca L, Cardoso JMS. Comparative Analysis of Bursaphelenchus xylophilus Secretome Under Pinus pinaster and P. pinea Stimuli. FRONTIERS IN PLANT SCIENCE 2021; 12:668064. [PMID: 34046053 PMCID: PMC8144518 DOI: 10.3389/fpls.2021.668064] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 03/29/2021] [Indexed: 05/19/2023]
Abstract
The pinewood nematode (PWN), Bursaphelenchus xylophilus, the pine wilt disease's (PWD) causal agent, is a migratory endoparasitic nematode skilled to feed on pine tissues and on fungi that colonize the trees. In order to study B. xylophilus secretomes under the stimulus of pine species with different susceptibilities to disease, nematodes were exposed to aqueous pine extracts from Pinus pinaster (high-susceptible host) and P. pinea (low-susceptible host). Sequential windowed acquisition of all theoretical mass spectra (SWATH-MS) was used to determine relative changes in protein amounts between B. xylophilus secretions, and a total of 776 secreted proteins were quantified in both secretomes. From these, 22 proteins were found increased in the B. xylophilus secretome under the P. pinaster stimulus and 501 proteins increased under the P. pinea stimulus. Functional analyses of the 22 proteins found increased in the P. pinaster stimulus showed that proteins with peptidase, hydrolase, and antioxidant activities were the most represented. On the other hand, gene ontology (GO) enrichment analysis of the 501 proteins increased under the P. pinea stimulus revealed an enrichment of proteins with binding activity. The differences detected in the secretomes highlighted the diverse responses from the nematode to overcome host defenses with different susceptibilities and provide new clues on the mechanism behind the pathogenicity of this plant-parasitic nematode. Proteomic data are available via ProteomeXchange with identifier PXD024011.
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Affiliation(s)
- Hugo Silva
- University of Coimbra, Centre for Functional Ecology, Department of Life Sciences, Coimbra, Portugal
| | - Sandra I. Anjo
- CNC – Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Bruno Manadas
- CNC – Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Isabel Abrantes
- University of Coimbra, Centre for Functional Ecology, Department of Life Sciences, Coimbra, Portugal
| | - Luís Fonseca
- University of Coimbra, Centre for Functional Ecology, Department of Life Sciences, Coimbra, Portugal
| | - Joana M. S. Cardoso
- University of Coimbra, Centre for Functional Ecology, Department of Life Sciences, Coimbra, Portugal
- *Correspondence: Joana M. S. Cardoso,
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32
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Ribeiro IP, Esteves L, Anjo SI, Marques F, Barroso L, Manadas B, Carreira IM, Melo JB. Proteomics-based Predictive Model for the Early Detection of Metastasis and Recurrence in Head and Neck Cancer. Cancer Genomics Proteomics 2020; 17:259-269. [PMID: 32345667 DOI: 10.21873/cgp.20186] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/04/2020] [Accepted: 02/07/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND/AIM Head and neck squamous cell carcinoma (HNSCC) presents high morbidity, an overall poor prognosis and survival, and a compromised quality of life of the survivors. Early tumor detection, prediction of its behavior and prognosis as well as the development of novel therapeutic strategies are urgently needed for a more successful HNSCC management. MATERIALS AND METHODS In this study, a proteomics analysis of HNSCC tumor and non-tumor samples was performed and a model to predict the risk of recurrence and metastasis development was built. RESULTS This predictive model presented good accuracy (>80%) and comprises as variables the tumor staging along with DHB12, HMGB3 and COBA1 proteins. Differences at the intensity levels of these proteins were correlated with the development of metastasis and recurrence as well as with patient's survival. CONCLUSION The translation of proteomic predictive models to routine clinical practice may contribute to a more precise and individualized clinical management of the HNSCC patients, reducing recurrences and improving patients' quality of life. The capability of generalization of this proteomic model to predict the recurrence and metastases development should be evaluated and validated in other HNSCC populations.
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Affiliation(s)
- Ilda Patrícia Ribeiro
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,iCBR-CIMAGO - Center of Investigation on Environment, Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Luísa Esteves
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Sandra Isabel Anjo
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Francisco Marques
- iCBR-CIMAGO - Center of Investigation on Environment, Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,Stomatology Unit, Coimbra Hospital and University Centre, CHUC, EPE, Coimbra, Portugal.,Department of Dentistry, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Leonor Barroso
- Maxillofacial Surgery Department, Coimbra Hospital and University Centre, CHUC, EPE, Coimbra, Portugal
| | - Bruno Manadas
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Isabel Marques Carreira
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,iCBR-CIMAGO - Center of Investigation on Environment, Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,CNC.IBILI, Group of Aging and Brain Diseases: Advanced Diagnosis and Biomarkers, Coimbra, Portugal
| | - Joana Barbosa Melo
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal .,iCBR-CIMAGO - Center of Investigation on Environment, Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,CNC.IBILI, Group of Aging and Brain Diseases: Advanced Diagnosis and Biomarkers, Coimbra, Portugal
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33
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Mancio J, Barros AS, Conceicão G, Santa C, Pessoa-Amorim G, Bartosch C, Fragao-Marques M, Ferreira W, Carvalho M, Ferreira N, Vouga L, Miranda IM, Vitorino R, Fontes-Carvalho R, Manadas B, Falcão-Pires I, Ribeiro VG, Leite-Moreira A, Bettencourt N. Influence of EPICardial adipose tissue in HEART diseases (EPICHEART) study: Protocol for a translational study in coronary atherosclerosis. Rev Port Cardiol 2020; 39:625-633. [PMID: 33168363 DOI: 10.1016/j.repc.2020.03.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 03/02/2020] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION Accumulation of epicardial adipose tissue (EAT) is associated with coronary artery disease (CAD) and increased risk of coronary events in asymptomatic subjects and low-risk patients, suggesting that EAT promotes atherosclerosis in its early stage. Recent studies have shown that the presence of CAD affects the properties of adjacent EAT, leading to dynamic changes in the molecular players involved in the interplay between EAT and the coronary arteries over the history of the disease. The role of EAT in late-stage CAD has not been investigated. OBJECTIVES In a comparative analysis with mediastinal and subcutaneous adipose tissue, we aim to investigate whether the volume of EAT assessed by computed tomography and its proteome assessed by SWATH-MS mass spectrometry are associated with late stages of CAD in an elderly cohort of severe aortic stenosis patients. METHODS The EPICHEART study (NCT03280433) is a prospective study enrolling patients with severe degenerative aortic stenosis referred for elective aortic valve replacement, whose protocol includes preoperative clinical, nutritional, echocardiographic, cardiac computed tomography and invasive coronary angiographic assessments. During cardiac surgery, samples of EAT and mediastinal and subcutaneous thoracic adipose tissue are collected for proteomics analysis by SWATH-MS. In addition, pericardial fluid and peripheral and coronary sinus blood samples are collected to identify circulating and local adipose tissue-derived biomarkers of CAD. CONCLUSION We designed a translational study to explore the association of EAT quantity and quality with advanced CAD. We expect to identify new biochemical factors and biomarkers in the crosstalk between EAT and the coronary arteries that are involved in the pathogenesis of late coronary atherosclerosis, especially coronary calcification, which might be translated into new therapeutic targets and imaging tools by biomedical engineering.
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Affiliation(s)
- Jennifer Mancio
- Department of Surgery and Physiology, Cardiovascular Research Unit (UnIC), Faculty of Medicine, University of Porto, Portugal; Department of Cardiology, Centro Hospitalar de Vila Nova de Gaia, Portugal.
| | - António S Barros
- Department of Surgery and Physiology, Cardiovascular Research Unit (UnIC), Faculty of Medicine, University of Porto, Portugal
| | - Glória Conceicão
- Department of Surgery and Physiology, Cardiovascular Research Unit (UnIC), Faculty of Medicine, University of Porto, Portugal
| | - Cátia Santa
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Guilherme Pessoa-Amorim
- Department of Surgery and Physiology, Cardiovascular Research Unit (UnIC), Faculty of Medicine, University of Porto, Portugal
| | - Carla Bartosch
- Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Mariana Fragao-Marques
- Department of Surgery and Physiology, Cardiovascular Research Unit (UnIC), Faculty of Medicine, University of Porto, Portugal
| | - Wilson Ferreira
- Department of Cardiology, Centro Hospitalar de Vila Nova de Gaia, Portugal
| | - Mónica Carvalho
- Department of Cardiology, Centro Hospitalar de Vila Nova de Gaia, Portugal
| | - Nuno Ferreira
- Department of Cardiology, Centro Hospitalar de Vila Nova de Gaia, Portugal
| | - Luís Vouga
- Department of Cardiothoracic Surgery, Centro Hospitalar de Vila Nova de Gaia, Portugal
| | - Isabel M Miranda
- Department of Surgery and Physiology, Cardiovascular Research Unit (UnIC), Faculty of Medicine, University of Porto, Portugal
| | - Rui Vitorino
- Department of Surgery and Physiology, Cardiovascular Research Unit (UnIC), Faculty of Medicine, University of Porto, Portugal
| | - Ricardo Fontes-Carvalho
- Department of Surgery and Physiology, Cardiovascular Research Unit (UnIC), Faculty of Medicine, University of Porto, Portugal; Department of Cardiology, Centro Hospitalar de Vila Nova de Gaia, Portugal
| | - Bruno Manadas
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Inês Falcão-Pires
- Department of Surgery and Physiology, Cardiovascular Research Unit (UnIC), Faculty of Medicine, University of Porto, Portugal
| | - Vasco Gama Ribeiro
- Department of Cardiology, Centro Hospitalar de Vila Nova de Gaia, Portugal
| | - Adelino Leite-Moreira
- Department of Surgery and Physiology, Cardiovascular Research Unit (UnIC), Faculty of Medicine, University of Porto, Portugal; Cardiothoracic Surgery, Centro Hospitalar de Sao João, Portugal
| | - Nuno Bettencourt
- Department of Surgery and Physiology, Cardiovascular Research Unit (UnIC), Faculty of Medicine, University of Porto, Portugal
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Influence of EPICardial adipose tissue in HEART diseases (EPICHEART) study: Protocol for a translational study in coronary atherosclerosis. REVISTA PORTUGUESA DE CARDIOLOGIA (ENGLISH EDITION) 2020. [DOI: 10.1016/j.repce.2020.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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35
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Domingues C, Geraldo AM, Anjo SI, Matos A, Almeida C, Caramelo I, Lopes-da-Silva JA, Paiva A, Carvalho J, Pires das Neves R, Manadas B, Grãos M. Cofilin-1 Is a Mechanosensitive Regulator of Transcription. Front Cell Dev Biol 2020; 8:678. [PMID: 32903827 PMCID: PMC7438942 DOI: 10.3389/fcell.2020.00678] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/06/2020] [Indexed: 12/11/2022] Open
Abstract
The mechanical properties of the extracellular environment are interrogated by cells and integrated through mechanotransduction. Many cellular processes depend on actomyosin-dependent contractility, which is influenced by the microenvironment’s stiffness. Here, we explored the influence of substrate stiffness on the proteome of proliferating undifferentiated human umbilical cord-matrix mesenchymal stem/stromal cells. The relative abundance of several proteins changed significantly by expanding cells on soft (∼3 kPa) or stiff substrates (GPa). Many such proteins are associated with the regulation of the actin cytoskeleton, a major player of mechanotransduction and cell physiology in response to mechanical cues. Specifically, Cofilin-1 levels were elevated in cells cultured on soft comparing with stiff substrates. Furthermore, Cofilin-1 was de-phosphorylated (active) and present in the nuclei of cells kept on soft substrates, in contrast with phosphorylated (inactive) and widespread distribution in cells on stiff. Soft substrates promoted Cofilin-1-dependent increased RNA transcription and faster RNA polymerase II-mediated transcription elongation. Cofilin-1 is part of a novel mechanism linking mechanotransduction and transcription.
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Affiliation(s)
- Catarina Domingues
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra (IIIUC), Coimbra, Portugal
| | - A Margarida Geraldo
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
| | - Sandra Isabel Anjo
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
| | - André Matos
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal.,Polytechnic Institute of Coimbra, Coimbra College of Agriculture, Coimbra, Portugal
| | - Cláudio Almeida
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal.,Polytechnic Institute of Coimbra, Coimbra College of Agriculture, Coimbra, Portugal
| | - Inês Caramelo
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra (IIIUC), Coimbra, Portugal
| | | | - Artur Paiva
- Flow Cytometry Unit, Department of Clinical Pathology, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal.,Coimbra Institute for Clinical and Biomedical Research, Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,Instituto Politécnico de Coimbra, ESTESC-Coimbra Health School, Ciências Biomédicas Laboratoriais, Coimbra, Portugal
| | - João Carvalho
- Centro de Física da Universidade de Coimbra (CFisUC), Department of Physics, University of Coimbra, Coimbra, Portugal
| | - Ricardo Pires das Neves
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra (IIIUC), Coimbra, Portugal
| | - Bruno Manadas
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
| | - Mário Grãos
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra (IIIUC), Coimbra, Portugal.,Biocant, Technology Transfer Association, Cantanhede, Portugal
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36
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Ribeiro M, Brigas HC, Temido-Ferreira M, Pousinha PA, Regen T, Santa C, Coelho JE, Marques-Morgado I, Valente CA, Omenetti S, Stockinger B, Waisman A, Manadas B, Lopes LV, Silva-Santos B, Ribot JC. Meningeal γδ T cell-derived IL-17 controls synaptic plasticity and short-term memory. Sci Immunol 2020; 4:4/40/eaay5199. [PMID: 31604844 DOI: 10.1126/sciimmunol.aay5199] [Citation(s) in RCA: 186] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/03/2019] [Indexed: 12/12/2022]
Abstract
The notion of "immune privilege" of the brain has been revised to accommodate its infiltration, at steady state, by immune cells that participate in normal neurophysiology. However, the immune mechanisms that regulate learning and memory remain poorly understood. Here, we show that noninflammatory interleukin-17 (IL-17) derived from a previously unknown fetal-derived meningeal-resident γδ T cell subset promotes cognition. When tested in classical spatial learning paradigms, mice lacking γδ T cells or IL-17 displayed deficient short-term memory while retaining long-term memory. The plasticity of glutamatergic synapses was reduced in the absence of IL-17, resulting in impaired long-term potentiation in the hippocampus. Conversely, IL-17 enhanced glial cell production of brain-derived neurotropic factor, whose exogenous provision rescued the synaptic and behavioral phenotypes of IL-17-deficient animals. Together, our work provides previously unknown clues on the mechanisms that regulate short-term versus long-term memory and on the evolutionary and functional link between the immune and nervous systems.
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Affiliation(s)
- Miguel Ribeiro
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Helena C Brigas
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Mariana Temido-Ferreira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Paula A Pousinha
- Institut de Pharmacologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique, Université de Côte d'Azur, Nice, France
| | - Tommy Regen
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Cátia Santa
- Center for Neuroscience and Cell Biology, Universidade de Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, Universidade de Coimbra, Coimbra, Portugal
| | - Joana E Coelho
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Inês Marques-Morgado
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Cláudia A Valente
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | | | | | - Ari Waisman
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Bruno Manadas
- Center for Neuroscience and Cell Biology, Universidade de Coimbra, Coimbra, Portugal
| | - Luísa V Lopes
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Bruno Silva-Santos
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
| | - Julie C Ribot
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
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Anjo SI, Dos Santos PV, Rosado L, Baltazar G, Baldeiras I, Pires D, Gomes A, Januário C, Castelo-Branco M, Grãos M, Manadas B. A different vision of translational research in biomarker discovery: a pilot study on circulatory mitochondrial proteins as Parkinson's disease potential biomarkers. Transl Neurodegener 2020; 9:11. [PMID: 32266064 PMCID: PMC7118951 DOI: 10.1186/s40035-020-00188-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 03/11/2020] [Indexed: 12/15/2022] Open
Abstract
Background The identification of circulating biomarkers that closely correlate with Parkinson’s Disease (PD) has failed several times in the past. Nevertheless, in this pilot study, a translational approach was conducted, allowing the evaluation of the plasma levels of two mitochondrial-related proteins, whose combination leads to a robust model with potential diagnostic value to discriminate the PD patients from matched controls. Methods The proposed translational approach was initiated by the analysis of secretomes from cells cultured under control or well-defined oxidative stress conditions, followed by the identification of proteins related to PD pathologic mechanisms that were altered between the two states. This pipeline was further translated into the analysis of undepleted plasma samples from 28 control and 31 PD patients. Results From the secretome analysis, several mitochondria-related proteins were found to be differentially released between control and stress conditions and to be able to distinguish the two secretomes. Similarly, two mitochondrial-related proteins were found to be significantly changed in a PD cohort compared to matched controls. Moreover, a linear discriminant model with potential diagnostic value to discriminate PD patients was obtained using the combination of these two proteins. Both proteins are associated with apoptotic mitochondrial changes, which may correspond to potential indicators of cell death. Moreover, one of these proteins, the VPS35 protein, was reported in plasma for the first time, and its quantification was only possible due to its previous identification in the secretome analysis. Conclusions In this work, an adaptation of a translational pipeline for biomarker selection was presented and transposed to neurological diseases, in the present case Parkinson’s Disease. The novelty and success of this pilot study may arise from the combination of: i) a translational research pipeline, where plasma samples are interrogated using knowledge previously obtained from the evaluation of cells’ secretome under oxidative stress; ii) the combined used of statistical analysis and an informed selection of candidates based on their link with relevant disease mechanisms, and iii) the use of SWATH-MS, an untargeted MS method that allows a complete record of the analyzed samples and a targeted data extraction of the quantitative values of proteins previously identified.
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Affiliation(s)
- Sandra I Anjo
- 1CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,2Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | | | - Luiza Rosado
- 4Centro Hospitalar Cova da Beira, E.P.E, Covilhã, Portugal
| | - Graça Baltazar
- 3Centro de Investigação em Ciências da Saúde (CICS-UBI), Universidade da Beira Interior, Covilhã, Portugal
| | - Inês Baldeiras
- 1CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,2Faculty of Medicine, University of Coimbra, Coimbra, Portugal.,5Neurology Department, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Diana Pires
- Coimbra Institute for Biomedical Imaging and Translational Research (CIBIT), Coimbra, Portugal
| | - Andreia Gomes
- Coimbra Institute for Biomedical Imaging and Translational Research (CIBIT), Coimbra, Portugal
| | - Cristina Januário
- 5Neurology Department, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Miguel Castelo-Branco
- Coimbra Institute for Biomedical Imaging and Translational Research (CIBIT), Coimbra, Portugal
| | - Mário Grãos
- 1CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,7Biocant, Biotechnology Transfer Association, Cantanhede, Portugal.,8Institute for Interdisciplinary Research, University of Coimbra (IIIUC), Coimbra, Portugal
| | - Bruno Manadas
- 1CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,8Institute for Interdisciplinary Research, University of Coimbra (IIIUC), Coimbra, Portugal
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Ferreira D, Escudeiro A, Adega F, Anjo SI, Manadas B, Chaves R. FA-SAT ncRNA interacts with PKM2 protein: depletion of this complex induces a switch from cell proliferation to apoptosis. Cell Mol Life Sci 2020; 77:1371-1386. [PMID: 31346634 PMCID: PMC11104958 DOI: 10.1007/s00018-019-03234-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/10/2019] [Accepted: 07/15/2019] [Indexed: 01/11/2023]
Abstract
FA-SAT is a highly conserved satellite DNA sequence transcribed in many Bilateria species. To disclose the cellular and functional profile of FA-SAT non-coding RNAs, a comprehensive experimental approach, including the transcripts location in the cell and in the cell cycle, the identification of its putative protein interactors, and silencing/ectopic expression phenotype analysis, was performed. FA-SAT non-coding RNAs play a nuclear function at the G1 phase of the cell cycle and the interactomic assay showed that the PKM2 protein is the main interactor. The disruption of the FA-SAT non-coding RNA/PKM2 protein complex, by the depletion of either FA-SAT or PKM2, results in the same phenotype-apoptosis, and the ectopic overexpression of FA-SAT did not affect the cell-cycle progression, but promotes the PKM2 nuclear accumulation. Overall, our data first describe the importance of this ribonucleoprotein complex in apoptosis and cell-cycle progression, what foresees a promising novel candidate molecular target for cancer therapy and diagnosis.
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Affiliation(s)
- Daniela Ferreira
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisbon, Portugal
| | - Ana Escudeiro
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisbon, Portugal
| | - Filomena Adega
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisbon, Portugal
| | - Sandra I Anjo
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
- Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
| | - Bruno Manadas
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
| | - Raquel Chaves
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal.
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisbon, Portugal.
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Barros D, Pradhan A, Pascoal C, Cássio F. Proteomic responses to silver nanoparticles vary with the fungal ecotype. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 704:135385. [PMID: 31787274 DOI: 10.1016/j.scitotenv.2019.135385] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/03/2019] [Accepted: 11/03/2019] [Indexed: 06/10/2023]
Abstract
Enhanced commercial application of silver nanoparticles (AgNPs) is increasing the chance of their release into aquatic environments, potentially putting non-target microorganisms at risk. Impacts of AgNPs and Ag+ on two fungal ecotypes of Articulospora tetracladia, collected from a metal-polluted (At61) and a non-polluted (At72) stream, were assessed based on antioxidant enzymatic and proteomic responses. At61 showed more tolerance to AgNPs than At72 (EC20, 158.9 vs 7.5 µg L-1, respectively). Antioxidant enzyme activities were induced by AgNPs or Ag+ in both fungal ecotypes. Proteomic responses to AgNPs or Ag+ revealed that 41.3% of the total altered proteins were common in At72, while 27.3% were common in At61. In At72, gene ontology enrichment analyses indicated that Ag+ increased mainly the content of proteins involved in proteostasis and decreased the content of those related to vesicle-mediated transport; whereas the key group of proteins induced by AgNPs had functions in DNA repair and energy production. In At61, AgNPs induced proteins involved in energy production and protein biosynthesis, while both Ag forms induced proteins related to cell-redox and protein homeostasis, ascospore formation, fatty acid biosynthesis and nucleic acids metabolism. Both Ag forms induced stress-responsive proteins, and this was consistent with the responses of antioxidant enzymes. The negligible quantity of Ag+ released from AgNPs (<0.2 μg L-1) supported a minor role of dissolved ionic form in AgNP-induced toxicity to both fungal ecotypes. Overall, results unraveled distinct mechanisms of toxicity and cellular targets of nanoparticulate and ionic silver in aquatic fungi with different environmental background, and constitutes a proof of concept that toxicants induce adaptive responses in microbes to face emergent contaminants.
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Affiliation(s)
- Diana Barros
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
| | - Arunava Pradhan
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal.
| | - Cláudia Pascoal
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
| | - Fernanda Cássio
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
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Graça I, Mendes VM, Marques I, Duro N, da Costa M, Ramalho JC, Pawlowski K, Manadas B, Pinto Ricardo CP, Ribeiro-Barros AI. Comparative Proteomic Analysis of Nodulated and Non-Nodulated Casuarina glauca Sieb. ex Spreng. Grown under Salinity Conditions Using Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS). Int J Mol Sci 2019; 21:E78. [PMID: 31861944 PMCID: PMC6982049 DOI: 10.3390/ijms21010078] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/15/2019] [Accepted: 12/18/2019] [Indexed: 12/25/2022] Open
Abstract
Casuarina glauca displays high levels of salt tolerance, but very little is known about how this tree adapts to saline conditions. To understand the molecular basis of C. glauca response to salt stress, we have analyzed the proteome from branchlets of plants nodulated by nitrogen-fixing Frankia Thr bacteria (NOD+) and non-nodulated plants supplied with KNO3 (KNO3+), exposed to 0, 200, 400, and 600 mM NaCl. Proteins were identified by Short Gel, Long Gradient Liquid Chromatography coupled to Tandem Mass Spectrometry and quantified by Sequential Window Acquisition of All Theoretical Mass Spectra -Mass Spectrometry. 600 proteins were identified and 357 quantified. Differentially Expressed Proteins (DEPs) were multifunctional and mainly involved in Carbohydrate Metabolism, Cellular Processes, and Environmental Information Processing. The number of DEPs increased gradually with stress severity: (i) from 7 (200 mM NaCl) to 40 (600 mM NaCl) in KNO3+; and (ii) from 6 (200 mM NaCl) to 23 (600 mM NaCl) in NOD+. Protein-protein interaction analysis identified different interacting proteins involved in general metabolic pathways as well as in the biosynthesis of secondary metabolites with different response networks related to salt stress. Salt tolerance in C. glauca is related to a moderate impact on the photosynthetic machinery (one of the first and most important stress targets) as well as to an enhancement of the antioxidant status that maintains cellular homeostasis.
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Affiliation(s)
- Inês Graça
- PlantStress&Biodiversity Lab, Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisbon, Portugal; (I.G.); (I.M.); (N.D.); (M.d.C.); (J.C.R.)
- Plant Biochemistry Lab, Instituto de Tecnologia Química e Biológica, Universidade NOVA de Lisboa, Av. República, Quinta do Marquês, 2780-157 Oeiras, Portugal;
| | - Vera M. Mendes
- CNC—Center for Neuroscience and Cell Biology, Universidade de Coimbra, UC Biotech—Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197 Cantanhede, Portugal; (V.M.M.); (B.M.)
| | - Isabel Marques
- PlantStress&Biodiversity Lab, Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisbon, Portugal; (I.G.); (I.M.); (N.D.); (M.d.C.); (J.C.R.)
| | - Nuno Duro
- PlantStress&Biodiversity Lab, Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisbon, Portugal; (I.G.); (I.M.); (N.D.); (M.d.C.); (J.C.R.)
- Plant Biochemistry Lab, Instituto de Tecnologia Química e Biológica, Universidade NOVA de Lisboa, Av. República, Quinta do Marquês, 2780-157 Oeiras, Portugal;
| | - Mário da Costa
- PlantStress&Biodiversity Lab, Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisbon, Portugal; (I.G.); (I.M.); (N.D.); (M.d.C.); (J.C.R.)
- Plant Biochemistry Lab, Instituto de Tecnologia Química e Biológica, Universidade NOVA de Lisboa, Av. República, Quinta do Marquês, 2780-157 Oeiras, Portugal;
| | - José C. Ramalho
- PlantStress&Biodiversity Lab, Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisbon, Portugal; (I.G.); (I.M.); (N.D.); (M.d.C.); (J.C.R.)
- GeoBioTec, Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), 2829-516 Caparica, Portugal
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden;
| | - Bruno Manadas
- CNC—Center for Neuroscience and Cell Biology, Universidade de Coimbra, UC Biotech—Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197 Cantanhede, Portugal; (V.M.M.); (B.M.)
| | - Cândido P. Pinto Ricardo
- Plant Biochemistry Lab, Instituto de Tecnologia Química e Biológica, Universidade NOVA de Lisboa, Av. República, Quinta do Marquês, 2780-157 Oeiras, Portugal;
| | - Ana I. Ribeiro-Barros
- PlantStress&Biodiversity Lab, Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisbon, Portugal; (I.G.); (I.M.); (N.D.); (M.d.C.); (J.C.R.)
- GeoBioTec, Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), 2829-516 Caparica, Portugal
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Anjo SI, Simões I, Castanheira P, Grãos M, Manadas B. Use of recombinant proteins as a simple and robust normalization method for untargeted proteomics screening: exhaustive performance assessment. Talanta 2019; 205:120163. [DOI: 10.1016/j.talanta.2019.120163] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/13/2019] [Accepted: 07/17/2019] [Indexed: 01/13/2023]
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Mancio J, Barros AS, Conceicao G, Pessoa-Amorim G, Santa C, Bartosch C, Ferreira W, Carvalho M, Ferreira N, Vouga L, Miranda IM, Vitorino R, Manadas B, Falcao-Pires I, Ribeiro VG, Leite-Moreira A, Bettencourt N. Epicardial adipose tissue volume and annexin A2/fetuin-A signalling are linked to coronary calcification in advanced coronary artery disease: Computed tomography and proteomic biomarkers from the EPICHEART study. Atherosclerosis 2019; 292:75-83. [PMID: 31783201 DOI: 10.1016/j.atherosclerosis.2019.11.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 10/27/2019] [Accepted: 11/13/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND & AIMS The role of epicardial adipose tissue (EAT) in the pathophysiology of late stage-coronary artery disease (CAD) has not been investigated. We explored the association of EAT volume and its proteome with advanced coronary atherosclerosis. METHODS The EPICHEART Study prospectively enrolled 574 severe aortic stenosis patients referred to cardiac surgery. Before surgery, EAT volume was quantified by computed tomography (CT). During surgery, epicardial, mediastinal (MAT) and subcutaneous (SAT) adipose tissue samples were collected to explore fat phenotype by analyzing the proteomic profile using SWATH-mass spectrometry; pericardial fluid and peripheral venous blood were also collected. CAD presence was defined as coronary artery stenosis ≥50% in invasive angiography and by CT-derived Agatston coronary calcium score (CCS). RESULTS EAT volume adjusted for body fat was associated with higher CCS, but not with the presence of coronary stenosis. In comparison with mediastinal and subcutaneous fat depots, EAT exhibited a pro-calcifying proteomic profile in patients with CAD characterized by upregulation of annexin-A2 and downregulation of fetuin-A; annexin-A2 protein levels in EAT samples were also positively correlated with CCS. We confirmed that the annexin-A2 gene was overexpressed in EAT samples of CAD patients and positively correlated with CCS. Fetuin-A gene was not detected in EAT samples, but systemic fetuin-A was higher in CAD than in non-CAD patients, suggesting that fetuin-A was locally downregulated. CONCLUSIONS In an elderly cohort of stable patients, CCS was associated with EAT volume and annexin-A2/fetuin-A signaling, suggesting that EAT might orchestrate pro-calcifying conditions in the late phases of CAD.
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Affiliation(s)
- Jennifer Mancio
- Department of Surgery and Physiology, Cardiovascular Research Unit (UnIC), Faculty of Medicine, University of Porto, Portugal; Department of Cardiology, Centro Hospitalar de Vila Nova de Gaia, Portugal.
| | - Antonio S Barros
- Department of Surgery and Physiology, Cardiovascular Research Unit (UnIC), Faculty of Medicine, University of Porto, Portugal
| | - Gloria Conceicao
- Department of Surgery and Physiology, Cardiovascular Research Unit (UnIC), Faculty of Medicine, University of Porto, Portugal
| | - Guilherme Pessoa-Amorim
- Department of Surgery and Physiology, Cardiovascular Research Unit (UnIC), Faculty of Medicine, University of Porto, Portugal
| | - Catia Santa
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; III: Institute for Interdisciplinary Research, University of Coimbra (IIIUC), Portugal
| | - Carla Bartosch
- Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Wilson Ferreira
- Department of Cardiology, Centro Hospitalar de Vila Nova de Gaia, Portugal
| | - Monica Carvalho
- Department of Cardiology, Centro Hospitalar de Vila Nova de Gaia, Portugal
| | - Nuno Ferreira
- Department of Cardiology, Centro Hospitalar de Vila Nova de Gaia, Portugal
| | - Luis Vouga
- Department of Cardiothoracic Surgery, Centro Hospitalar de Vila Nova de Gaia, Portugal
| | - Isabel M Miranda
- Department of Surgery and Physiology, Cardiovascular Research Unit (UnIC), Faculty of Medicine, University of Porto, Portugal
| | - Rui Vitorino
- Department of Surgery and Physiology, Cardiovascular Research Unit (UnIC), Faculty of Medicine, University of Porto, Portugal
| | - Bruno Manadas
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Ines Falcao-Pires
- Department of Surgery and Physiology, Cardiovascular Research Unit (UnIC), Faculty of Medicine, University of Porto, Portugal
| | - Vasco Gama Ribeiro
- Department of Cardiology, Centro Hospitalar de Vila Nova de Gaia, Portugal
| | - Adelino Leite-Moreira
- Department of Surgery and Physiology, Cardiovascular Research Unit (UnIC), Faculty of Medicine, University of Porto, Portugal; Department of Cardiothoracic Surgery, Centro Hospitalar de Sao Joao, Portugal
| | - Nuno Bettencourt
- Department of Surgery and Physiology, Cardiovascular Research Unit (UnIC), Faculty of Medicine, University of Porto, Portugal
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Anjos L, Pinto PIS, Tsironi T, Dimopoulos G, Santos S, Santa C, Manadas B, Canario A, Taoukis P, Power DM. Experimental data from flesh quality assessment and shelf life monitoring of high pressure processed European sea bass ( Dicentrarchus labrax) fillets. Data Brief 2019; 26:104451. [PMID: 31667223 PMCID: PMC6811897 DOI: 10.1016/j.dib.2019.104451] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/07/2019] [Accepted: 08/21/2019] [Indexed: 11/27/2022] Open
Abstract
Fresh fish are highly perishable food products and their short shelf-life limits their commercial exploitation and leads to waste, which has a negative impact on aquaculture sustainability. New non-thermal food processing methods, such as high pressure (HP) processing, prolong shelf-life while assuring high food quality. The effect of HP processing (600MPa, 25 °C, 5min) on European sea bass (Dicentrarchus labrax) fillet quality and shelf life was investigated. The data presented comprises microbiome and proteome profiles of control and HP-processed sea bass fillets from 1 to 67 days of isothermal storage at 2 °C. Bacterial diversity was analysed by Illumina high-throughput sequencing of the 16S rRNA gene in pooled DNAs from control or HP-processed fillets after 1, 11 or 67 days and the raw reads were deposited in the NCBI-SRA database with accession number PRJNA517618. Yeast and fungi diversity were analysed by high-throughput sequencing of the internal transcribed spacer (ITS) region for control and HP-processed fillets at the end of storage (11 or 67 days, respectively) and have the SRA accession number PRJNA517779. Quantitative label-free proteomics profiles were analysed by SWATH-MS (Sequential Windowed data independent Acquisition of the Total High-resolution-Mass Spectra) in myofibrillar or sarcoplasmic enriched protein extracts pooled for control or HP-processed fillets after 1, 11 and 67 days of storage. Proteome data was deposited in the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD012737. These data support the findings reported in the associated manuscript “High pressure processing of European sea bass (Dicentrarchus labrax) fillets and tools for flesh quality and shelf life monitoring”, Tsironi et al., 2019, JFE 262:83–91, doi.org/10.1016/j.jfoodeng.2019.05.010.
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Affiliation(s)
- Liliana Anjos
- Comparative Endocrinology and Integrative Biology Group (CEIB), Centro de Ciencias do Mar (CCMAR), University of Algarve, Faro, Portugal
| | - Patricia I S Pinto
- Comparative Endocrinology and Integrative Biology Group (CEIB), Centro de Ciencias do Mar (CCMAR), University of Algarve, Faro, Portugal
| | - Theofania Tsironi
- Laboratory of Food Chemistry and Technology, School of Chemical Engineering, National Technical University of Athens (NTUA), Greece
| | - George Dimopoulos
- Laboratory of Food Chemistry and Technology, School of Chemical Engineering, National Technical University of Athens (NTUA), Greece
| | - Soraia Santos
- Comparative Endocrinology and Integrative Biology Group (CEIB), Centro de Ciencias do Mar (CCMAR), University of Algarve, Faro, Portugal
| | - Cátia Santa
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra (IIIUC), Portugal
| | - Bruno Manadas
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Portugal
| | - Adelino Canario
- Comparative Endocrinology and Integrative Biology Group (CEIB), Centro de Ciencias do Mar (CCMAR), University of Algarve, Faro, Portugal
| | - Petros Taoukis
- Laboratory of Food Chemistry and Technology, School of Chemical Engineering, National Technical University of Athens (NTUA), Greece
| | - Deborah M Power
- Comparative Endocrinology and Integrative Biology Group (CEIB), Centro de Ciencias do Mar (CCMAR), University of Algarve, Faro, Portugal
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Curto P, Santa C, Allen P, Manadas B, Simões I, Martinez JJ. A Pathogen and a Non-pathogen Spotted Fever Group Rickettsia Trigger Differential Proteome Signatures in Macrophages. Front Cell Infect Microbiol 2019; 9:43. [PMID: 30895174 PMCID: PMC6414445 DOI: 10.3389/fcimb.2019.00043] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 02/11/2019] [Indexed: 12/13/2022] Open
Abstract
We have previously reported that Rickettsia conorii and Rickettsia montanensis have distinct intracellular fates within THP-1 macrophages, suggesting that the ability to proliferate within macrophages may be a distinguishable factor between pathogenic and non-pathogenic Spotted fever group (SFG) members. To start unraveling the molecular mechanisms underlying the capacity (or not) of SFG Rickettsia to establish their replicative niche in macrophages, we have herein used quantitative proteomics by SWATH-MS to profile the alterations resulted by the challenge of THP-1 macrophages with R. conorii and R. montanensis. We show that the pathogenic, R. conorii, and the non-pathogenic, R. montanensis, member of SFG Rickettsia trigger differential proteomic signatures in macrophage-like cells upon infection. R. conorii specifically induced the accumulation of several enzymes of the tricarboxylic acid cycle, oxidative phosphorylation, fatty acid β-oxidation, and glutaminolysis, as well as of several inner and outer membrane mitochondrial transporters. These results suggest a profound metabolic rewriting of macrophages by R. conorii toward a metabolic signature of an M2-like, anti-inflammatory activation program. Moreover, several subunits forming the proteasome and immunoproteasome are found in lower abundance upon infection with both rickettsial species, which may help bacteria to escape immune surveillance. R. conorii-infection specifically induced the accumulation of several host proteins implicated in protein processing and quality control in ER, suggesting that this pathogenic Rickettsia may be able to increase the ER protein folding capacity. This work reveals novel aspects of macrophage-Rickettsia interactions, expanding our knowledge of how pathogenic rickettsiae explore host cells to their advantage.
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Affiliation(s)
- Pedro Curto
- PhD Programme in Experimental Biology and Biomedicine, Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Vector Borne Disease Laboratories, Department of Pathobiological Sciences, LSU School of Veterinary Medicine, Baton Rouge, LA, United States
| | - Cátia Santa
- Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Paige Allen
- Vector Borne Disease Laboratories, Department of Pathobiological Sciences, LSU School of Veterinary Medicine, Baton Rouge, LA, United States
| | - Bruno Manadas
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Isaura Simões
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Vector Borne Disease Laboratories, Department of Pathobiological Sciences, LSU School of Veterinary Medicine, Baton Rouge, LA, United States
| | - Juan J. Martinez
- Vector Borne Disease Laboratories, Department of Pathobiological Sciences, LSU School of Veterinary Medicine, Baton Rouge, LA, United States
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Anjo SI, Melo MN, Loureiro LR, Sabala L, Castanheira P, Grãos M, Manadas B. oxSWATH: An integrative method for a comprehensive redox-centered analysis combined with a generic differential proteomics screening. Redox Biol 2019; 22:101130. [PMID: 30737169 PMCID: PMC6435957 DOI: 10.1016/j.redox.2019.101130] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 01/27/2019] [Accepted: 01/28/2019] [Indexed: 12/21/2022] Open
Abstract
Most of the redox proteomics strategies are focused on the identification and relative quantification of cysteine oxidation without considering the variation in the total levels of the proteins. However, protein synthesis and protein degradation also belong to the regulatory mechanisms of the cells, being therefore important to consider the changes in total protein levels in PTMs-focused analyses, such as cysteine redox characterization. Therefore, a novel integrative approach combining the SWATH-MS method with differential alkylation using a combination of commonly available alkylating reagents (oxSWATH) is presented, by which it is possible to integrate the information regarding relative cysteine oxidation with the analysis of the total protein levels in a cost-effective high-throughput approach. The proposed method was tested using a redox-regulated protein and further applied to a comparative analysis of secretomes obtained from cells cultured under control or oxidative stress conditions to strengthen the importance of considering the overall proteome changes. Using the OxSWATH method it was possible to determine both the relative proportion of reduced and reversible oxidized oxoforms, as well as the total levels of each oxoform by taking into consideration the total levels of the protein. Therefore, using OxSWATH the comparative analyses can be performed at two different levels by considering the relative proportion or the total levels at both peptide and protein level. Moreover, since samples are acquired in SWATH-MS mode, besides the redox centered analysis, a generic differential protein expression analysis can also be performed, allowing a truly comprehensive evaluation of proteomics changes upon the oxidative stimulus. Data are available via ProteomeXchange and SWATHAtlas with the identifiers PXD006802, PXD006802, and PASS01210. Determination of redox changes considering protein total levels. Integrative redoxomics and common differential proteomics in a single analysis. Differential alkylation strategy using commonly available alkylating agents. First untargeted label-free quantitative method to study cysteine oxidation.
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Affiliation(s)
- Sandra I Anjo
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal; Faculty of Medicine, University of Coimbra, Coimbra, Portugal.
| | - Matilde N Melo
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Liliana R Loureiro
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Lúcia Sabala
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | | | - Mário Grãos
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Biocant, Technology Transfer Association, Cantanhede, Portugal
| | - Bruno Manadas
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
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Anjo SI, Santa C, Manadas B. SWATH Mass Spectrometry Applied to Cerebrospinal Fluid Differential Proteomics: Establishment of a Sample-Specific Method. Methods Mol Biol 2019; 2044:169-189. [PMID: 31432413 DOI: 10.1007/978-1-4939-9706-0_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Mass spectrometry (MS) has become the gold standard method for proteomics by allowing the simultaneous identification and/or quantification of thousands of proteins of a given sample. Over time, mass spectrometry has evolved into newer quantitative approaches with increased sensitivity and accuracy, such as the sequential windows acquisition of all theoretical fragment-ion spectra (SWATH)-MS approach. Moreover, in the past few years, some improvements were made in the SWATH-acquisition algorithm, allowing the design of sample-customized acquisition methods by adjusting the Q1 windows' width in order to reduce it in the most populated m/z regions. This customization results in an increase in the specificity and a reduction in the interferences, ultimately leading to an improvement in the amount of quantitative data extracted to eventually increase the proteome coverage. These improvements are especially relevant for clinical neuroproteomics, which is mainly based on the analysis of circulatory biofluids, in particular the cerebrospinal fluid (CSF) due to its close connection with the brain.In the present chapter, a detailed description of the methodologies necessary to perform a whole-proteome relative quantification of CSF samples by SWATH-MS is presented, starting with the isolation of the protein fraction, its preparation for MS analysis, with all the necessary information for the design of a SWATH-MS method specific for each sample batch, and finally providing different methodologies for the analysis of the quantitative data obtained.
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Affiliation(s)
- Sandra I Anjo
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Cátia Santa
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Bruno Manadas
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.
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Influence of passage number on the impact of the secretome of adipose tissue stem cells on neural survival, neurodifferentiation and axonal growth. Biochimie 2018; 155:119-128. [PMID: 30342112 DOI: 10.1016/j.biochi.2018.09.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 09/13/2018] [Accepted: 09/20/2018] [Indexed: 02/07/2023]
Abstract
Mesenchymal stem cells (MSCs), and within them adipose tissue derived stem cells (ASCs), have been shown to have therapeutic effects on central nervous system (CNS) cell populations. Such effects have been mostly attributed to soluble factors, as well as vesicles, present in their secretome. Yet, little is known about the impact that MSC passaging might have in the secretion therapeutic profile. Our aim was to show how human ASCs (hASCs) passage number influences the effect of their secretome in neuronal survival, differentiation and axonal growth. For this purpose, post-natal rat hippocampal primary cultures, human neural progenitor cell (hNPCs) cultures and dorsal root ganglia (DRGs) explants were incubated with secretome, collected as conditioned media (CM), obtained from hASCs in P3, P6, P9 and P12. Results showed no differences when comparing percentages of MAP-2 positive cells (a mature neuronal marker) in neuronal cultures or hNPCs, after incubation with hASCs secretome from different passages. The same was observed regarding DRG neurite outgrowth. In order to characterize the secretomes obtained from different passages, a proteomic analysis was performed, revealing that its composition did not vary significantly with passage number P3 to P12. Results allowed us to identify several key proteins, such as pigment epithelium derived factor (PEDF), DJ-1, interleucin-6 (IL-6) and galectin, all of which have already proven to play neuroprotective and neurodifferentiating roles. Proteins that promote neurite outgrowth were also found present, such as semaphorin 7A and glypican-1. We conclude that cellular passaging does not influence significantly hASCs's secretome properties especially their ability to support post-natal neuronal survival, induce neurodifferentiation and promote axonal growth.
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Mendes-Pinheiro B, Teixeira FG, Anjo SI, Manadas B, Behie LA, Salgado AJ. Secretome of Undifferentiated Neural Progenitor Cells Induces Histological and Motor Improvements in a Rat Model of Parkinson's Disease. Stem Cells Transl Med 2018; 7:829-838. [PMID: 30238668 PMCID: PMC6216452 DOI: 10.1002/sctm.18-0009] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 06/07/2018] [Accepted: 06/18/2018] [Indexed: 01/04/2023] Open
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative movement disorder that results from the death of dopamine (DA) neurons. Over recent years, differentiated or undifferentiated neural stem cells (NSCs) transplantation has been widely used as a means of cell replacement therapy. However, compelling evidence has brought attention to the array of bioactive molecules produced by stem cells, defined as secretome. As described in the literature, other cell populations have a high‐neurotrophic activity, but little is known about NSCs. Moreover, the exploration of the stem cell secretome is only in its initial stages, particularly as applied to neurodegenerative diseases. Thus, we have characterized the secretome of human neural progenitor cells (hNPCs) through proteomic analysis and investigated its effects in a 6‐hydroxidopamine (6‐OHDA) rat model of PD in comparison with undifferentiated hNPCs transplantation. Results revealed that the injection of hNPCs secretome potentiated the histological recovery of DA neurons when compared to the untreated group 6‐OHDA and those transplanted with cells (hNPCs), thereby supporting the functional motor amelioration of 6‐OHDA PD animals. Additionally, hNPCs secretome proteomic characterization has revealed that these cells have the capacity to secrete a wide range of important molecules with neuroregulatory actions, which are most likely support the effects observed. Overall, we have concluded that the use of hNPCs secretome partially modulate DA neurons cell survival and ameliorate PD animals’ motor deficits, disclosing improved results when compared to cell transplantation approaches, indicating that the secretome itself could represent a route for new therapeutic options for PD regenerative medicine. stem cells translational medicine2018;7:829–838
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Affiliation(s)
- Bárbara Mendes-Pinheiro
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Guimarães, Portugal
| | - Fábio G Teixeira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Guimarães, Portugal
| | - Sandra I Anjo
- Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal.,CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Bruno Manadas
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Leo A Behie
- Pharmaceutical Production Research Facility, Schulich School of Engineering, University of Calgary, Calgary, Alberta, Canada
| | - António J Salgado
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Guimarães, Portugal
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Elucidation of the dynamic nature of interactome networks: A practical tutorial. J Proteomics 2018; 171:116-126. [DOI: 10.1016/j.jprot.2017.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/23/2017] [Accepted: 04/10/2017] [Indexed: 01/12/2023]
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50
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STAGE-Diging in Proteomics. Methods Mol Biol 2017. [PMID: 28986796 DOI: 10.1007/978-1-4939-7231-9_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Proteomics is nowadays a standard tool in life sciences for the analysis of protein abundance, modifications and interactions but has so far failed to enter the clinic for routine applications. New generation mass spectrometers and chromatographic systems are able to cover approximately an entire cell proteome in one run but sample preparation, in terms of time and sample recovery, is still a critical step. Here we describe a modification of the in-gel digestion method, called STAGE-diging, that reduces sample handling, decreases the analysis time and improves protein identification and quantification. This method is particularly useful for those research labs that manage different biological samples and have a limited access to MS instrumentation or are required to perform high-throughput analysis in short time like a clinical laboratory.
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