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Iglesias MJ, Schwenk JM, Odeberg J. Affinity Proteomics Assays for Cardiovascular and Atherosclerotic Disease Biomarkers. Methods Mol Biol 2021; 2344:163-179. [PMID: 34115359 DOI: 10.1007/978-1-0716-1562-1_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Systematic exploration of the dynamic human plasma proteome enables the discovery of novel protein biomarkers. Using state-of-the-art technologies holds the promise to facilitate a better diagnosis and risk prediction of diseases. Cardiovascular disease (CVD) pathophysiology is characterized for unbalancing of processes such as vascular inflammation, endothelial dysfunction, or lipid profiles among others. Such processes have a direct impact on the dynamic and complex composition of blood and hence the plasma proteome. Therefore, the study of the plasma proteome comprises an excellent exploratory source of biomarker research particularly for CVD. We describe the protocol for performing the discovery of protein biomarker candidates using the suspension bead array technology. The process does not require depletion steps to remove abundant proteins and consumes only a few microliters of sample from the body fluid of interest. The approach is scalable to measure many analytes as well as large numbers of samples. Moreover, we describe a bead-assisted antibody-labeling process that helps to develop quantitative assays for validation purposes and facilitate the translation of the identified candidates into clinical studies.
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Affiliation(s)
- Maria Jesus Iglesias
- Science for Life Laboratory, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden. .,Department of Clinical Medicine, Faculty of Health Science, The Arctic University of Tromsø, Tromsø, Norway.
| | - Jochen M Schwenk
- Science for Life Laboratory, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Jacob Odeberg
- Science for Life Laboratory, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden.,Department of Clinical Medicine, Faculty of Health Science, The Arctic University of Tromsø, Tromsø, Norway.,Department of Medicine, Karolinska Institutet, Stockholm, Sweden
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Bachmann J, Burté F, Pramana S, Conte I, Brown BJ, Orimadegun AE, Ajetunmobi WA, Afolabi NK, Akinkunmi F, Omokhodion S, Akinbami FO, Shokunbi WA, Kampf C, Pawitan Y, Uhlén M, Sodeinde O, Schwenk JM, Wahlgren M, Fernandez-Reyes D, Nilsson P. Affinity proteomics reveals elevated muscle proteins in plasma of children with cerebral malaria. PLoS Pathog 2014; 10:e1004038. [PMID: 24743550 PMCID: PMC3990714 DOI: 10.1371/journal.ppat.1004038] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 02/06/2014] [Indexed: 01/21/2023] Open
Abstract
Systemic inflammation and sequestration of parasitized erythrocytes are central processes in the pathophysiology of severe Plasmodium falciparum childhood malaria. However, it is still not understood why some children are more at risks to develop malaria complications than others. To identify human proteins in plasma related to childhood malaria syndromes, multiplex antibody suspension bead arrays were employed. Out of the 1,015 proteins analyzed in plasma from more than 700 children, 41 differed between malaria infected children and community controls, whereas 13 discriminated uncomplicated malaria from severe malaria syndromes. Markers of oxidative stress were found related to severe malaria anemia while markers of endothelial activation, platelet adhesion and muscular damage were identified in relation to children with cerebral malaria. These findings suggest the presence of generalized vascular inflammation, vascular wall modulations, activation of endothelium and unbalanced glucose metabolism in severe malaria. The increased levels of specific muscle proteins in plasma implicate potential muscle damage and microvasculature lesions during the course of cerebral malaria. Why do some malaria-infected children develop severe and lethal forms of the disease, while others only have mild forms? In order to try to find potential answers or clues to this question, we have here analyzed more than 1,000 different human proteins in the blood of more than 500 malaria-infected children from Ibadan in Nigeria, a holoendemic malaria region. We identified several proteins that were present at higher levels in the blood from the children that developed severe malaria in comparison to those that did not. Some of the most interesting identified proteins were muscle specific proteins, which indicate that damaged muscles could be a discriminatory pathologic event in cerebral malaria compared to other malaria cases. These findings will hopefully lead to an increased understanding of the disease and may contribute to the development of clinical algorithms that could predict which children are more at risks to severe malaria. This in turn will be of high value in the management of these children in already overloaded tertiary-care health facilities in urban large densely-populated sub-Saharan cities with holoendemic malaria such as in the case of Ibadan and Lagos.
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Affiliation(s)
- Julie Bachmann
- SciLifeLab Stockholm, School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Florence Burté
- Division of Parasitology, Medical Research Council National Institute for Medical Research, London, United Kingdom
| | - Setia Pramana
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ianina Conte
- Division of Parasitology, Medical Research Council National Institute for Medical Research, London, United Kingdom
| | - Biobele J. Brown
- Department of Paediatrics, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
- Department of Haematology, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
- Childhood Malaria Research Group, University College Hospital, Ibadan, Nigeria
| | - Adebola E. Orimadegun
- Department of Paediatrics, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
| | - Wasiu A. Ajetunmobi
- Department of Paediatrics, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
| | - Nathaniel K. Afolabi
- Department of Paediatrics, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
| | - Francis Akinkunmi
- Department of Paediatrics, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
| | - Samuel Omokhodion
- Department of Paediatrics, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
- Childhood Malaria Research Group, University College Hospital, Ibadan, Nigeria
| | - Felix O. Akinbami
- Department of Paediatrics, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
- Childhood Malaria Research Group, University College Hospital, Ibadan, Nigeria
| | - Wuraola A. Shokunbi
- Department of Haematology, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
- Childhood Malaria Research Group, University College Hospital, Ibadan, Nigeria
| | - Caroline Kampf
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Yudi Pawitan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mathias Uhlén
- SciLifeLab Stockholm, School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Olugbemiro Sodeinde
- Division of Parasitology, Medical Research Council National Institute for Medical Research, London, United Kingdom
- Department of Paediatrics, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
- Department of Haematology, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
- Childhood Malaria Research Group, University College Hospital, Ibadan, Nigeria
| | - Jochen M. Schwenk
- SciLifeLab Stockholm, School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Mats Wahlgren
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- * E-mail: (MW); (DFR); (PN)
| | - Delmiro Fernandez-Reyes
- Division of Parasitology, Medical Research Council National Institute for Medical Research, London, United Kingdom
- Department of Paediatrics, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
- Department of Haematology, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
- Childhood Malaria Research Group, University College Hospital, Ibadan, Nigeria
- Brighton & Sussex Medical School, Sussex University, Brighton, United Kingdom
- * E-mail: (MW); (DFR); (PN)
| | - Peter Nilsson
- SciLifeLab Stockholm, School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
- * E-mail: (MW); (DFR); (PN)
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