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Drack A, Rai A, Greening DW. Generation of Red Blood Cell Nanovesicles as a Delivery Tool. Methods Mol Biol 2023; 2628:321-336. [PMID: 36781795 DOI: 10.1007/978-1-0716-2978-9_21] [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] [Indexed: 02/15/2023]
Abstract
Extracellular vesicles (EVs) are natural membranous vesicles with immense potential as drug delivery tools. However, their large-scale production remains a huge technical challenge, is time consuming, and expensive. Thus, EV mimetics (nanovesicles) generated from easily sourced red blood cells (RBCs) have gained vested interest as an effective and scalable drug delivery system. Their surface proteins (e.g., CD47) inherited from parental RBCs also improve their biocompatibility and bioavailability. Here, we outline a step-by-step guide for large-scale production of RBC nanovesicles using one-step extrusion method coupled to rapid density-cushion centrifugation. We also outline protocol for their extensive biophysical characterization (size and morphology using single particle analysis and cryogenic electron microscopy), and in-depth mass spectrometry-based proteome characterization. Finally, we outline two strategies (active loading during extrusion vs. passive loading via diffusion) to incorporate pharmacological compound(s) into nanovesicles and detect their loading using spectrophotometry.
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Affiliation(s)
- Auriane Drack
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Department of Biochemistry and Chemistry, La Trobe University, Melbourne, VIC, Australia
| | - Alin Rai
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Baker Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, VIC, Australia
| | - David W Greening
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.
- Department of Biochemistry and Chemistry, La Trobe University, Melbourne, VIC, Australia.
- Baker Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, VIC, Australia.
- Central Clinical School, Monash University, Melbourne, VIC, Australia.
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, VIC, Australia.
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2
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Dziekan JM, Wirjanata G, Dai L, Go KD, Yu H, Lim YT, Chen L, Wang LC, Puspita B, Prabhu N, Sobota RM, Nordlund P, Bozdech Z. Cellular thermal shift assay for the identification of drug-target interactions in the Plasmodium falciparum proteome. Nat Protoc 2020; 15:1881-1921. [PMID: 32341577 DOI: 10.1038/s41596-020-0310-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 01/13/2020] [Indexed: 02/06/2023]
Abstract
Despite decades of research, little is known about the cellular targets and the mode of action of the vast majority of antimalarial drugs. We recently demonstrated that the cellular thermal shift assay (CETSA) protocol in its two variants: the melt curve and the isothermal dose-response, represents a comprehensive strategy for the identification of antimalarial drug targets. CETSA enables proteome-wide target screening for unmodified antimalarial compounds with undetermined mechanisms of action, providing quantitative evidence about direct drug-protein interactions. The experimental workflow involves treatment of P. falciparum-infected erythrocytes with a compound of interest, heat exposure to denature proteins, soluble protein isolation, enzymatic digestion, peptide labeling with tandem mass tags, offline fractionation, and liquid chromatography-tandem mass spectrometry analysis. Methodological optimizations necessary for the analysis of this intracellular parasite are discussed, including enrichment of parasitized cells and hemoglobin depletion strategies to overcome high hemoglobin abundance in the host red blood cells. We outline an effective data processing workflow using the mineCETSA R package, which enables prioritization of drug-target candidates for follow-up studies. The entire protocol can be completed within 2 weeks.
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Affiliation(s)
- Jerzy Michal Dziekan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Grennady Wirjanata
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Lingyun Dai
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,The Second Clinical Medical College of Jinan University, First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, China
| | - Ka Diam Go
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Han Yu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yan Ting Lim
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Liyan Chen
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Loo Chien Wang
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Brenda Puspita
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Nayana Prabhu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Radoslaw M Sobota
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore. .,Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
| | - Pär Nordlund
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore. .,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore. .,Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden.
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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3
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Klatt S, Roberts A, Lothian A, Masters CL, Cappai R, Fowler C, Roberts BR. Optimizing red blood cell protein extraction for biomarker quantitation with mass spectrometry. Anal Bioanal Chem 2020; 412:1879-1892. [PMID: 32030493 DOI: 10.1007/s00216-020-02439-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/11/2020] [Accepted: 01/17/2020] [Indexed: 10/25/2022]
Abstract
Red blood cells (RBC) are the most common cell type found in blood. They might serve as reservoir for biomarker research as they are anuclear and lack the ability to synthesize proteins. Not many biomarker assays, however, have been conducted on RBC because of their large dynamic range of proteins, high abundance of lipids, and hemoglobin interferences. Here, we developed a semiquantitative mass spectrometry-based assay that targeted 144 proteins and compared the efficiency of urea, sodium deoxycholate, acetonitrile, and HemoVoid™ in their extraction of the RBC proteome. Our results indicate that protein extraction with HemoVoid™ led to hemoglobin reduction and increased detection of low abundance proteins. Although hemoglobin interference after deoxycholate and urea extraction was high, there were adequate amounts of low abundance proteins for quantitation. Extraction with acetonitrile led to an overall decrease in protein abundances probably as a result of precipitation. Overall, the best compromise in sensitivity and sample processing time was achieved with the urea-trypsin digestion protocol. This provided the basis for large-scale evaluations of protein targets as potential blood-based biomarkers. As a proof of concept, we applied this assay to determine that alpha-synuclein, a prominent marker in Parkinson's disease, has an average concentration of approximately 40 μg mL-1 in RBC. This is important to know as the concentration of alpha-synuclein in plasma, typically in the picogram per milliliter range, might be partially derived from lysed RBC. Utilization of this assay will prove useful for future biomarker studies and provide a more complete analytical toolbox for the measurement of blood-derived proteins. Graphical abstract.
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Affiliation(s)
- Stephan Klatt
- The Florey Institute of Neuroscience and Mental Health, Melbourne Dementia Research Centre, The University of Melbourne, 30 Royal Parade, Parkville, Victoria, 3052, Australia.,Cooperative Research Centre for Mental Health, Parkville, Victoria, 3052, Australia
| | - Anne Roberts
- The Florey Institute of Neuroscience and Mental Health, Melbourne Dementia Research Centre, The University of Melbourne, 30 Royal Parade, Parkville, Victoria, 3052, Australia.,Cooperative Research Centre for Mental Health, Parkville, Victoria, 3052, Australia
| | - Amber Lothian
- The Florey Institute of Neuroscience and Mental Health, Melbourne Dementia Research Centre, The University of Melbourne, 30 Royal Parade, Parkville, Victoria, 3052, Australia.,Cooperative Research Centre for Mental Health, Parkville, Victoria, 3052, Australia
| | - Colin L Masters
- The Florey Institute of Neuroscience and Mental Health, Melbourne Dementia Research Centre, The University of Melbourne, 30 Royal Parade, Parkville, Victoria, 3052, Australia.,Cooperative Research Centre for Mental Health, Parkville, Victoria, 3052, Australia
| | - Roberto Cappai
- Department of Pharmacology and Therapeutics, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Christopher Fowler
- The Florey Institute of Neuroscience and Mental Health, Melbourne Dementia Research Centre, The University of Melbourne, 30 Royal Parade, Parkville, Victoria, 3052, Australia.,Cooperative Research Centre for Mental Health, Parkville, Victoria, 3052, Australia
| | - Blaine R Roberts
- The Florey Institute of Neuroscience and Mental Health, Melbourne Dementia Research Centre, The University of Melbourne, 30 Royal Parade, Parkville, Victoria, 3052, Australia. .,Cooperative Research Centre for Mental Health, Parkville, Victoria, 3052, Australia. .,Department of Biochemistry, Department of Neurology, School of Medicine, Emory University, Atlanta, GA, 30322, USA.
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Keren-Aviram G, Dachet F, Bagla S, Balan K, Loeb JA, Dratz EA. Proteomic analysis of human epileptic neocortex predicts vascular and glial changes in epileptic regions. PLoS One 2018; 13:e0195639. [PMID: 29634780 PMCID: PMC5892923 DOI: 10.1371/journal.pone.0195639] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 03/26/2018] [Indexed: 01/21/2023] Open
Abstract
Epilepsy is a common neurological disorder, which is not well understood at the molecular level. Exactly why some brain regions produce epileptic discharges and others do not is not known. Patients who fail to respond to antiseizure medication (refractory epilepsy) can benefit from surgical removal of brain regions to reduce seizure frequency. The tissue removed in these surgeries offers an invaluable resource to uncover the molecular and cellular basis of human epilepsy. Here, we report a proteomic study to determine whether there are common proteomic patterns in human brain regions that produce epileptic discharges. We analyzed human brain samples, as part of the Systems Biology of Epilepsy Project (SBEP). These brain pieces are in vivo electrophysiologically characterized human brain samples withdrawn from the neocortex of six patients with refractory epilepsy. This study is unique in that for each of these six patients the comparison of protein expression was made within the same patient: a more epileptic region was compared to a less epileptic brain region. The amount of epileptic activity was defined for each patient as the frequency of their interictal spikes (electric activity between seizures that is a parameter strongly linked to epilepsy). Proteins were resolved from three subcellular fractions, using a 2D differential gel electrophoresis (2D-DIGE), revealing 31 identified protein spots that changed significantly. Interestingly, glial fibrillary acidic protein (GFAP) was found to be consistently down regulated in high spiking brain tissue and showed a strong negative correlation with spike frequency. We also developed a two-step analysis method to select for protein species that changed frequently among the patients and identified these proteins. A total of 397 protein spots of interest (SOI) were clustered by protein expression patterns across all samples. These clusters were used as markers and this analysis predicted proteomic changes due to both histological differences and molecular pathways, revealed by examination of gene ontology clusters. Our experimental design and proteomic data analysis predicts novel glial changes, increased angiogenesis, and changes in cytoskeleton and neuronal projections between high and low interictal spiking regions. Quantitative histological staining of these same tissues for both the vascular and glial changes confirmed these findings, which provide new insights into the structural and functional basis of neocortical epilepsy.
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Affiliation(s)
- Gal Keren-Aviram
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana, United States of America
| | - Fabien Dachet
- The Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- Department of Neurology and Rehabilitation, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Shruti Bagla
- The Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Karina Balan
- The Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Jeffrey A. Loeb
- The Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- Department of Neurology and Rehabilitation, University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail:
| | - Edward A. Dratz
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana, United States of America
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In Silico Functional Networks Identified in Fish Nucleated Red Blood Cells by Means of Transcriptomic and Proteomic Profiling. Genes (Basel) 2018; 9:genes9040202. [PMID: 29642539 PMCID: PMC5924544 DOI: 10.3390/genes9040202] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 03/22/2018] [Accepted: 03/29/2018] [Indexed: 12/17/2022] Open
Abstract
Nucleated red blood cells (RBCs) of fish have, in the last decade, been implicated in several immune-related functions, such as antiviral response, phagocytosis or cytokine-mediated signaling. RNA-sequencing (RNA-seq) and label-free shotgun proteomic analyses were carried out for in silico functional pathway profiling of rainbow trout RBCs. For RNA-seq, a de novo assembly was conducted, in order to create a transcriptome database for RBCs. For proteome profiling, we developed a proteomic method that combined: (a) fractionation into cytosolic and membrane fractions, (b) hemoglobin removal of the cytosolic fraction, (c) protein digestion, and (d) a novel step with pH reversed-phase peptide fractionation and final Liquid Chromatography Electrospray Ionization Tandem Mass Spectrometric (LC ESI-MS/MS) analysis of each fraction. Combined transcriptome- and proteome- sequencing data identified, in silico, novel and striking immune functional networks for rainbow trout nucleated RBCs, which are mainly linked to innate and adaptive immunity. Functional pathways related to regulation of hematopoietic cell differentiation, antigen presentation via major histocompatibility complex class II (MHCII), leukocyte differentiation and regulation of leukocyte activation were identified. These preliminary findings further implicate nucleated RBCs in immune function, such as antigen presentation and leukocyte activation.
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Nombela I, Puente-Marin S, Chico V, Villena AJ, Carracedo B, Ciordia S, Mena MC, Mercado L, Perez L, Coll J, Estepa A, Ortega-Villaizan MDM. Identification of diverse defense mechanisms in rainbow trout red blood cells in response to halted replication of VHS virus. F1000Res 2017; 6:1958. [PMID: 29527292 PMCID: PMC5820608 DOI: 10.12688/f1000research.12985.2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/31/2018] [Indexed: 01/14/2023] Open
Abstract
Background: It has been described that fish nucleated red blood cells (RBCs) generate a wide variety of immune-related gene transcripts when viruses highly replicate inside them and are their main target cell. The immune response and mechanisms of fish RBCs against viruses targeting other cells or tissues has not yet been explored and is the objective of our study. Methods: Rainbow trout RBCs were obtained from peripheral blood, ficoll purified and exposed to Viral Haemorrhagic Septicaemia virus (VHSV). Immune response was evaluated by means of RT-qPCR, flow cytometry, immunofluorescence and isobaric tag for relative and absolute quantification (iTRAQ) protein profiling. Results: VHSV N gene transcripts incremented early postexposure and were drastically decreased after 6 hours postexposure (hpe). The expression of type I interferon ( ifn1) gene was significantly downregulated at early postexposure (3 hpe), together with a gradual downregulation of interferon-inducible mx and pkr genes until 72 hpe. Type I IFN protein was downregulated and interferon-inducible Mx protein was maintained at basal levels. Co-culture assays of RBCs, previously exposed to UV-inactivated VHSV, and TSS (stromal cell line from spleen) revealed IFN crosstalk between both cell types. On the other hand, anti-microbial peptide β-defensin 1 and neutrophil chemotactic factor interleukin 8 were slightly upregulated in VHSV-exposed RBCs. iTRAQ profiling revealed that VHSV exposure can induce a global protein downregulation in rainbow trout RBCs, mainly related to RNA stability and proteasome pathways. Antioxidant/antiviral response is also suggested to be involved in the response of rainbow trout RBCs to VHSV. Conclusions: A variety of mechanisms are proposed to be implicated in the antiviral response of rainbow trout RBCs against VHSV halted infection. Ongoing research is focused on understanding the mechanisms in detail.
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Affiliation(s)
- Ivan Nombela
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Spain
| | - Sara Puente-Marin
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Spain
| | - Veronica Chico
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Spain
| | - Alberto J. Villena
- Área de Biología Celular, Departamento de Biología Molecular, Universidad de León, León, Spain
| | - Begoña Carracedo
- Área de Biología Celular, Departamento de Biología Molecular, Universidad de León, León, Spain
| | - Sergio Ciordia
- Unidad de Proteómica, Centro Nacional de Biotecnología, Madrid, Spain
| | - Maria Carmen Mena
- Unidad de Proteómica, Centro Nacional de Biotecnología, Madrid, Spain
| | - Luis Mercado
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Luis Perez
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Spain
| | | | - Amparo Estepa
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Spain
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7
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Nombela I, Puente-Marin S, Chico V, Villena AJ, Carracedo B, Ciordia S, Mena MC, Mercado L, Perez L, Coll J, Estepa A, Ortega-Villaizan MDM. Identification of diverse defense mechanisms in trout red blood cells in response to VHSV halted viral replication. F1000Res 2017; 6:1958. [PMID: 29527292 PMCID: PMC5820608 DOI: 10.12688/f1000research.12985.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/01/2017] [Indexed: 01/09/2023] Open
Abstract
Background: It has been described that fish nucleated red blood cells (RBCs) generate a wide variety of immune-related gene transcripts when viruses highly replicate inside them and are their main target cell. The immune response and mechanisms of fish RBCs against viruses targeting other cells or tissues has not yet been explored and is the objective of our study. Methods: Trout RBCs were obtained from peripheral blood, ficoll purified and exposed to Viral Haemorrhagic Septicaemia virus (VHSV). Immune response was evaluated by means of RT-qPCR, flow cytometry, immunofluorescence and isobaric tag for relative and absolute quantification (iTRAQ) protein profiling Results: VHSV N gene transcripts incremented early postexposure and were drastically decreased after 6 hours postexposure (hpe). The expression of the type I interferon ( ifn1) gene was significantly downregulated at early postexposure (3 hpe), together with a gradual downregulation of interferon-inducible mx and pkr genes until 72 hpe. Type I IFN protein was downregulated and interferon-inducible Mx protein was maintained at basal levels. Co-culture assays of RBCs with TSS (stromal cell line from spleen) revealed the IFN crosstalk between both cell types. On the other hand, anti-microbial peptide β-defensin 1 and neutrophil chemotactic factor interleukin 8 were slightly upregulated in VHSV-exposed RBCs Isobaric tag for relative and absolute quantification (iTRAQ) revealed that VHSV exposure can induce a global protein downregulation in trout RBCs, mainly related to RNA stability and proteasome pathways. The antioxidant/antiviral response is also suggested to be involved in the response of trout RBCs to VHSV. Conclusions: A variety of mechanisms are proposed to be implicated in the antiviral response of trout RBCs against VHSV halted infection. Ongoing research is focused on understanding the mechanisms in detail. To our knowledge, this is the first report that implicates fish RBCs in the antiviral response against viruses not targeting RBCs.
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Affiliation(s)
- Ivan Nombela
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Spain
| | - Sara Puente-Marin
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Spain
| | - Veronica Chico
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Spain
| | - Alberto J. Villena
- Área de Biología Celular, Departamento de Biología Molecular, Universidad de León, León, Spain
| | - Begoña Carracedo
- Área de Biología Celular, Departamento de Biología Molecular, Universidad de León, León, Spain
| | - Sergio Ciordia
- Unidad de Proteómica, Centro Nacional de Biotecnología, Madrid, Spain
| | - Maria Carmen Mena
- Unidad de Proteómica, Centro Nacional de Biotecnología, Madrid, Spain
| | - Luis Mercado
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Luis Perez
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Spain
| | | | - Amparo Estepa
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Spain
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Vicente Miranda H, Cássio R, Correia-Guedes L, Gomes MA, Chegão A, Miranda E, Soares T, Coelho M, Rosa MM, Ferreira JJ, Outeiro TF. Posttranslational modifications of blood-derived alpha-synuclein as biochemical markers for Parkinson's disease. Sci Rep 2017; 7:13713. [PMID: 29057912 PMCID: PMC5651848 DOI: 10.1038/s41598-017-14175-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 10/05/2017] [Indexed: 11/24/2022] Open
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disorder known for the typical motor features associated. Pathologically, it is characterized by the intracellular accumulation of alpha-synuclein (aSyn) in Lewy bodies and Lewy neurites. Currently, there are no established biochemical markers for diagnosing or for following disease progression, a major limitation for the clinical practice. Posttranslational modifications (PTMs) in aSyn have been identified and implicated on its pathobiology. Since aSyn is abundant in blood erythrocytes, we aimed to evaluate whether PTMs of aSyn in the blood might hold value as a biomarker for PD. We examined 58 patients with PD and 30 healthy age-matched individuals. We found that the levels of Y125 phosphorylated, Y39 nitrated, and glycated aSyn were increased in PD, while those of SUMO were reduced. A combinatory analysis of the levels of these PTMs resulted in an increased sensitivity, with an area under curve (AUC) of 0.843 for PD versus healthy controls, and correlated with disease severity and duration. We conclude that the levels of these selected PTMs hold strong potential as biochemical markers for PD. Ultimately, our findings might facilitate the monitoring of disease progression in clinical trials, opening the possibility for developing more effective therapies against PD.
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Affiliation(s)
- Hugo Vicente Miranda
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School|Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056, Lisboa, Portugal.
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
| | - Rafaela Cássio
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Leonor Correia-Guedes
- Clinical Pharmacology Unit, Instituto de Medicina Molecular, Lisbon, Portugal
- Department of Neurosciences and Mental Health, Neurology, Hospital de Santa Maria-CHLN, Lisbon, Portugal
| | - Marcos António Gomes
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Ana Chegão
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School|Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056, Lisboa, Portugal
| | - Elisa Miranda
- Clinical Pharmacology Unit, Instituto de Medicina Molecular, Lisbon, Portugal
| | - Tiago Soares
- Clinical Pharmacology Unit, Instituto de Medicina Molecular, Lisbon, Portugal
| | - Miguel Coelho
- Clinical Pharmacology Unit, Instituto de Medicina Molecular, Lisbon, Portugal
- Department of Neurosciences and Mental Health, Neurology, Hospital de Santa Maria-CHLN, Lisbon, Portugal
| | - Mário Miguel Rosa
- Clinical Pharmacology Unit, Instituto de Medicina Molecular, Lisbon, Portugal
- Department of Neurosciences and Mental Health, Neurology, Hospital de Santa Maria-CHLN, Lisbon, Portugal
| | - Joaquim J Ferreira
- Clinical Pharmacology Unit, Instituto de Medicina Molecular, Lisbon, Portugal
| | - Tiago Fleming Outeiro
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School|Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056, Lisboa, Portugal.
- Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Waldweg 33, 37073, Göttingen, Germany.
- Max Planck Institute for Experimental Medicine, Göttingen, Germany.
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D'Alessandro A, Zolla L. Proteomic analysis of red blood cells and the potential for the clinic: what have we learned so far? Expert Rev Proteomics 2017; 14:243-252. [PMID: 28162022 DOI: 10.1080/14789450.2017.1291347] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
INTRODUCTION Red blood cells (RBC) are the most abundant host cells in the human body. Mature erythrocytes are devoid of nuclei and organelles and have always been regarded as circulating 'bags of hemoglobin'. The advent of proteomics has challenged this assumption, revealing unanticipated complexity and novel roles for RBCs not just in gas transport, but also in systemic metabolic homeostasis in health and disease. Areas covered: In this review we will summarize the main advancements in the field of discovery mode and redox/quantitative proteomics with respect to RBC biology. We thus focus on translational/clinical applications, such as transfusion medicine, hematology (e.g. hemoglobinopathies) and personalized medicine. Synergy of omics technologies - especially proteomics and metabolomics - are highlighted as a hallmark of clinical metabolomics applications for the foreseeable future. Expert commentary: The introduction of advanced proteomics technologies, especially quantitative and redox proteomics, and the integration of proteomics data with omics information gathered through orthogonal technologies (especially metabolomics) promise to revolutionize many biomedical areas, from hematology and transfusion medicine to personalized medicine and clinical biochemistry.
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Affiliation(s)
- Angelo D'Alessandro
- a Department of Biochemistry and Molecular Genetics , University of Colorado Denver - Anschutz Medical Campus , Aurora , CO , USA
| | - Lello Zolla
- b Department of Ecological and Biological Sciences , Universita' degli Studi della Tuscia , Viterbo , Italy
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10
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Abstract
Red blood cells (RBCs) are known for their role in oxygen and carbon dioxide transport. The main function of RBCs is directly linked to many diseases that cause low oxygen levels in tissues such as congenital heart disease in adults, chronic obstructive pulmonary disease, sleep apnea, sickle cell disease, etc. Red blood cells are a direct target for a number of parasitic diseases such as malaria (Plasmodium) and similar parasites of the phylum Apicomplexa (Toxoplasma, Theileria, Eimeria, Babesia, and Cryptosporidium). RBC membrane components, in particular, are suitable targets for the discovery of drugs against parasite interaction. There is also evidence that RBCs release growth and survival factors, thereby linking RBCs with cancer. RBCs are abundant and travel throughout the body; consequently changes in RBC proteome potentially reflect other diseases as well. This chapter describes erythrocyte isolation from blood and its fractionation into RBC membrane and soluble cytosolic fractions. Alternative procedures for mass spectrometry analysis of RBC membrane proteome will be presented.
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Affiliation(s)
- Ana Sofia Carvalho
- Computational and Experimental Biology Group, Nova Medical School/ Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Rua Câmara Pestana, 6-6A, Lisboa, 1150-082, Portugal
| | - Manuel S Rodriguez
- Advanced Technology Institute in Life Sciences (ITAV), CNRS-USR3505, 31106, Toulouse, France
- University of Toulouse III-Paul Sabatier, 31077, Toulouse, France
| | - Rune Matthiesen
- Computational and Experimental Biology Group, CEDOC-Chronic Diseases Research Center, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Rua Câmara Pestana, 6-6A, Lisboa, 1150-082, Portugal.
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Weisenhorn EMM, van T Erve TJ, Riley NM, Hess JR, Raife TJ, Coon JJ. Multi-omics Evidence for Inheritance of Energy Pathways in Red Blood Cells. Mol Cell Proteomics 2016; 15:3614-3623. [PMID: 27777340 DOI: 10.1074/mcp.m116.062349] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 10/21/2016] [Indexed: 12/21/2022] Open
Abstract
Each year over 90 million units of blood are transfused worldwide. Our dependence on this blood supply mandates optimized blood management and storage. During storage, red blood cells undergo degenerative processes resulting in altered metabolic characteristics which may make blood less viable for transfusion. However, not all stored blood spoils at the same rate, a difference that has been attributed to variable rates of energy usage and metabolism in red blood cells. Specific metabolite abundances are heritable traits; however, the link between heritability of energy metabolism and red blood cell storage profiles is unclear. Herein we performed a comprehensive metabolomics and proteomics study of red blood cells from 18 mono- and di-zygotic twin pairs to measure heritability and identify correlations with ATP and other molecular indices of energy metabolism. Without using affinity-based hemoglobin depletion, our work afforded the deepest multi-omic characterization of red blood cell membranes to date (1280 membrane proteins and 330 metabolites), with 119 membrane protein and 148 metabolite concentrations found to be over 30% heritable. We demonstrate a high degree of heritability in the concentration of energy metabolism metabolites, especially glycolytic metabolites. In addition to being heritable, proteins and metabolites involved in glycolysis and redox metabolism are highly correlated, suggesting that crucial energy metabolism pathways are inherited en bloc at distinct levels. We conclude that individuals can inherit a phenotype composed of higher or lower concentrations of these proteins together. This can result in vastly different red blood cells storage profiles which may need to be considered to develop precise and individualized storage options. Beyond guiding proper blood storage, this intimate link in heritability between energy and redox metabolism pathways may someday prove useful in determining the predisposition of an individual toward metabolic diseases.
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Affiliation(s)
- Erin M M Weisenhorn
- From the ‡Integrated Program in Biochemistry.,§Biomolecular Chemistry.,**Genome Center, University of Wisconsin, Madison, Wisconsin, 53706
| | - Thomas J van T Erve
- ‡‡Interdisciplinary Graduate Program in Human Toxicology, The University of Iowa, Iowa City, Iowa 52242
| | - Nicholas M Riley
- ¶Departments of Chemistry.,**Genome Center, University of Wisconsin, Madison, Wisconsin, 53706
| | - John R Hess
- §§Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195
| | | | - Joshua J Coon
- §Biomolecular Chemistry, .,¶Departments of Chemistry.,**Genome Center, University of Wisconsin, Madison, Wisconsin, 53706
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12
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Chakrabarti A, Halder S, Karmakar S. Erythrocyte and platelet proteomics in hematological disorders. Proteomics Clin Appl 2016; 10:403-14. [PMID: 26611378 DOI: 10.1002/prca.201500080] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 10/26/2015] [Accepted: 11/19/2015] [Indexed: 12/20/2022]
Abstract
Erythrocytes undergo ineffective erythropoesis, hemolysis, and premature eryptosis in sickle cell disease and thalassemia. Abnormal hemoglobin variants associated with hemoglobinopathy lead to vesiculation, membrane instability, and loss of membrane asymmetry with exposal of phosphatidylserine. This potentiates thrombin generation resulting in activation of the coagulation cascade responsible for subclinical phenotypes. Platelet activation also results in the release of microparticles, which express and transfer functional receptors from platelet membrane, playing key roles in vascular reactivity and activation of intracellular signaling pathways. Over the last decade, proteomics had proven to be an important field of research in studies of blood and blood diseases. Blood cells and its fluidic components have been proven to be easy systems for studying differential expressions of proteins in hematological diseases encompassing hemoglobinopathies, different types of anemias, myeloproliferative disorders, and coagulopathies. Proteomic studies of erythrocytes and platelets reported from several groups have highlighted various factors that intersect the signaling networks in these anucleate systems. In this review, we have elaborated on the current scenario of anucleate blood cell proteomes in normal and diseased individuals and the cross-talk between the two major constituent cell types of circulating blood.
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Affiliation(s)
- Abhijit Chakrabarti
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Suchismita Halder
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Shilpita Karmakar
- Biophysics and Structural Genomics Division, Saha institute of Nuclear Physics, Kolkata, India
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13
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Derazshamshir A, Baydemir G, Yılmaz F, Bereli N, Denizli A. Preparation of cryogel columns for depletion of hemoglobin from human blood. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2016; 44:792-9. [DOI: 10.3109/21691401.2015.1129623] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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14
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Barasa B, Slijper M. Challenges for red blood cell biomarker discovery through proteomics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1844:1003-10. [PMID: 24129076 DOI: 10.1016/j.bbapap.2013.10.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 09/11/2013] [Accepted: 10/01/2013] [Indexed: 12/23/2022]
Abstract
Red blood cells are rather unique body cells, since they have lost all organelles when mature, which results in lack of potential to replace proteins that have lost their function. They maintain only a few pathways for obtaining energy and reducing power for the key functions they need to fulfill. This makes RBCs highly sensitive to any aberration. If so, these RBCs are quickly removed from circulation, but if the RBC levels reduce extremely fast, this results in hemolytic anemia. Several causes of HA exist, and proteome analysis is the most straightforward way to obtain deeper insight into RBC functioning under the stress of disease. This should result in discovery of biomarkers, typical for each source of anemia. In this review, several challenges to generate in-depth RBC proteomes are described, like to obtain pure RBCs, to overcome the wide dynamic range in protein expression, and to establish which of the identified/quantified proteins are active in RBCs. The final challenge is to acquire and validate suited biomarkers unique for the changes that occur for each of the clinical questions; in red blood cell aging (also important for transfusion medicine), for thalassemias or sickle cell disease. Biomarkers for other hemolytic anemias that are caused by dysfunction of RBC membrane proteins (the RBC membrane defects) or RBC cytosolic proteins (the enzymopathies) are sometimes even harder to discover, in particular for the patients with RBC rare diseases with unknown cause. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.
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Affiliation(s)
- Benjamin Barasa
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH, The Netherlands
| | - Monique Slijper
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH, The Netherlands.
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15
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Walpurgis K, Kohler M, Thomas A, Wenzel F, Geyer H, Schänzer W, Thevis M. Effects of gamma irradiation and 15 days of subsequent ex vivo storage on the cytosolic red blood cell proteome analyzed by 2D-DIGE and Orbitrap MS. Proteomics Clin Appl 2013; 7:561-70. [PMID: 23670890 DOI: 10.1002/prca.201300009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 03/01/2013] [Accepted: 03/30/2013] [Indexed: 12/20/2022]
Abstract
PURPOSE Gamma irradiation of red blood cell (RBC) concentrates is routinely used to prevent transfusion-associated graft-versus-host disease. So far, the effects of ionizing radiation on RBC structure and function and especially the proteome are not fully understood. EXPERIMENTAL DESIGN RBC concentrates were irradiated with 30 Gy and stored for 1 or 15 days at 4 ± 2°C. Following cell lysis and hemoglobin depletion, 2D-DIGE was used to examine the changes of the cytosolic RBC proteome. Significantly altered spots were analyzed using bottom-up proteomic approaches and selected marker proteins validated by western blotting. RESULTS Gamma irradiation was found to enhance conventional RBC storage lesions. Following 15 days of postirradiation storage, the abundances of a total of 27 spots were significantly altered and 3 out of 13 identified proteins were selected and validated as potential marker proteins for the assessment of irradiation-induced cytosolic RBC lesions. CONCLUSIONS AND CLINICAL RELEVANCE Gamma irradiation and subsequent ex vivo storage according to the Council of Europe guidelines were found to affect RBC protein structures. The validated marker proteins can serve as a basis for the development of a screening assay to monitor the quality of irradiated RBC concentrates during ex vivo storage.
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Affiliation(s)
- Katja Walpurgis
- Center for Preventive Doping Research/Institute of Biochemistry, German Sport University Cologne, Germany
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16
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Pallotta V, D’Alessandro A, Rinalducci S, Zolla L. Native Protein Complexes in the Cytoplasm of Red Blood Cells. J Proteome Res 2013; 12:3529-46. [DOI: 10.1021/pr400431b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Valeria Pallotta
- Department of Ecological
and Biological Sciences, University of Tuscia, Largo dell’Università,
snc, 01100 Viterbo, Italy
| | - Angelo D’Alessandro
- Department of Ecological
and Biological Sciences, University of Tuscia, Largo dell’Università,
snc, 01100 Viterbo, Italy
| | - Sara Rinalducci
- Department of Ecological
and Biological Sciences, University of Tuscia, Largo dell’Università,
snc, 01100 Viterbo, Italy
| | - Lello Zolla
- Department of Ecological
and Biological Sciences, University of Tuscia, Largo dell’Università,
snc, 01100 Viterbo, Italy
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17
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Walpurgis K, Kohler M, Thomas A, Wenzel F, Geyer H, Schänzer W, Thevis M. Storage-induced changes of the cytosolic red blood cell proteome analyzed by 2D DIGE and high-resolution/high-accuracy MS. Proteomics 2012; 12:3263-72. [DOI: 10.1002/pmic.201200280] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Revised: 08/15/2012] [Accepted: 08/22/2012] [Indexed: 12/17/2022]
Affiliation(s)
- Katja Walpurgis
- Center for Preventive Doping Research/Institute of Biochemistry; German Sport University Cologne; Germany
| | - Maxie Kohler
- Department of Chemistry; University of Cologne; Germany
| | - Andreas Thomas
- Center for Preventive Doping Research/Institute of Biochemistry; German Sport University Cologne; Germany
| | - Folker Wenzel
- Institute of Transplantation Diagnostics and Cell Therapeutics; University of Düsseldorf Medical School; Düsseldorf Germany
| | - Hans Geyer
- Center for Preventive Doping Research/Institute of Biochemistry; German Sport University Cologne; Germany
| | - Wilhelm Schänzer
- Center for Preventive Doping Research/Institute of Biochemistry; German Sport University Cologne; Germany
| | - Mario Thevis
- Center for Preventive Doping Research/Institute of Biochemistry; German Sport University Cologne; Germany
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