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Rinschen MM, Saez-Rodriguez J. The tissue proteome in the multi-omic landscape of kidney disease. Nat Rev Nephrol 2020; 17:205-219. [PMID: 33028957 DOI: 10.1038/s41581-020-00348-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2020] [Indexed: 02/07/2023]
Abstract
Kidney research is entering an era of 'big data' and molecular omics data can provide comprehensive insights into the molecular footprints of cells. In contrast to transcriptomics, proteomics and metabolomics generate data that relate more directly to the pathological symptoms and clinical parameters observed in patients. Owing to its complexity, the proteome still holds many secrets, but has great potential for the identification of drug targets. Proteomics can provide information about protein synthesis, modification and degradation, as well as insight into the physical interactions between proteins, and between proteins and other biomolecules. Thus far, proteomics in nephrology has largely focused on the discovery and validation of biomarkers, but the systematic analysis of the nephroproteome can offer substantial additional insights, including the discovery of mechanisms that trigger and propagate kidney disease. Moreover, proteome acquisition might provide a diagnostic tool that complements the assessment of a kidney biopsy sample by a pathologist. Such applications are becoming increasingly feasible with the development of high-throughput and high-coverage technologies, such as versatile mass spectrometry-based techniques and protein arrays, and encourage further proteomics research in nephrology.
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Affiliation(s)
- Markus M Rinschen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark. .,III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany. .,Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany. .,Department of Chemistry, Scripps Center for Metabolomics and Mass Spectrometry, Scripps Research, La Jolla, CA, USA.
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University, and Heidelberg University Hospital, Bioquant, Heidelberg, Germany.,Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, Aachen, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory and Heidelberg University, Heidelberg, Germany
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Nicolaou O, Sokratous K, Makowska Z, Morell M, De Groof A, Montigny P, Hadjisavvas A, Michailidou K, Oulas A, Spyrou GM, Demetriou C, Alarcón-Riquelme ME, Psarellis S, Kousios A, Lauwerys B, Kyriacou K. Proteomic analysis in lupus mice identifies Coronin-1A as a potential biomarker for lupus nephritis. Arthritis Res Ther 2020; 22:147. [PMID: 32552896 PMCID: PMC7301983 DOI: 10.1186/s13075-020-02236-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/03/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Approximately 50% of systemic lupus erythematosus (SLE) patients develop nephritis, which is among the most severe and frequent complications of the disease and a leading cause of morbidity and mortality. Despite intensive research, there are still no reliable lupus nephritis (LN) markers in clinical use that can assess renal damage and activity with a high sensitivity and specificity. To this end, the aim of this study was to identify new clinically relevant tissue-specific protein biomarkers and possible underlying molecular mechanisms associated with renal involvement in SLE, using mass spectrometry (MS)-based proteomics. METHODS Kidneys were harvested from female triple congenic B6.NZMsle1/sle2/sle3 lupus mice model, and the respective sex- and age-matched C57BL/6 control mice at 12, 24 and 36 weeks of age, representing pre-symptomatic, established and end-stage LN, respectively. Proteins were extracted from kidneys, purified, reduced, alkylated and digested by trypsin. Purified peptides were separated by liquid chromatography and analysed by high-resolution MS. Data were processed by the Progenesis QIp software, and functional annotation analysis was performed using DAVID bioinformatics resources. Immunofluorescence and multiple reaction monitoring (MRM) MS methods were used to confirm prospective biomarkers in SLE mouse strains as well as human serum samples. RESULTS Proteomic profiling of kidney tissues from SLE and control mice resulted in the identification of more than 3800 unique proteins. Pathway analysis revealed a number of dysregulated molecular pathways that may be mechanistically involved in renal pathology, including phagosome and proximal tubule bicarbonate reclamation pathways. Proteomic analysis supported by human transcriptomic data and pathway analysis revealed Coronin-1A, Ubiquitin-like protein ISG15, and Rho GDP-dissociation inhibitor 2, as potential LN biomarkers. These results were further validated in other SLE mouse strains using MRM-MS. Most importantly, experiments in humans showed that measurement of Coronin-1A in human sera using MRM-MS can segregate LN patients from SLE patients without nephritis with a high sensitivity (100%) and specificity (100%). CONCLUSIONS These preliminary findings suggest that serum Coronin-1A may serve as a promising non-invasive biomarker for LN and, upon validation in larger cohorts, may be employed in the future as a screening test for renal disease in SLE patients.
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Affiliation(s)
- Orthodoxia Nicolaou
- Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Iroon Avenue 6, Agios Dometios, 2371, P.O. Box 23462 / 1683, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Iroon Avenue 6, Agios Dometios, 2371, P.O. Box 23462 / 1683, Nicosia, Cyprus
| | - Kleitos Sokratous
- Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Iroon Avenue 6, Agios Dometios, 2371, P.O. Box 23462 / 1683, Nicosia, Cyprus
- Bioinformatics Group, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Present Address: OMass Therapeutics, The Schrödinger Building, Heatley Road, The Oxford Science Park, Oxford, OX4 4GE, UK
| | | | - María Morell
- Genomic Medicine Department, Centre for Genomics and Oncological Research (GENYO), Pfizer-University of Granada-Andalusian Regional Government, Granada, Spain
| | - Aurélie De Groof
- Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, Brussels, Belgium
| | - Pauline Montigny
- Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, Brussels, Belgium
- CHU UCL Namur, Yvoir, Belgium
| | - Andreas Hadjisavvas
- Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Iroon Avenue 6, Agios Dometios, 2371, P.O. Box 23462 / 1683, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Iroon Avenue 6, Agios Dometios, 2371, P.O. Box 23462 / 1683, Nicosia, Cyprus
| | - Kyriaki Michailidou
- Cyprus School of Molecular Medicine, Iroon Avenue 6, Agios Dometios, 2371, P.O. Box 23462 / 1683, Nicosia, Cyprus
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Anastasis Oulas
- Cyprus School of Molecular Medicine, Iroon Avenue 6, Agios Dometios, 2371, P.O. Box 23462 / 1683, Nicosia, Cyprus
- Bioinformatics Group, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - George M Spyrou
- Cyprus School of Molecular Medicine, Iroon Avenue 6, Agios Dometios, 2371, P.O. Box 23462 / 1683, Nicosia, Cyprus
- Bioinformatics Group, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Christiana Demetriou
- Department of Primary Care and Population Health, University of Nicosia Medical School, Nicosia, Cyprus
| | - Marta E Alarcón-Riquelme
- Genomic Medicine Department, Centre for Genomics and Oncological Research (GENYO), Pfizer-University of Granada-Andalusian Regional Government, Granada, Spain
- Unit of Immunology and Chronic Disease, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Savvas Psarellis
- Department of Rheumatology, Nicosia General Hospital, Nicosia, Cyprus
| | - Andreas Kousios
- Renal and Transplant Centre Hammersmith Hospital Imperial College Healthcare NHS Trust, London, UK
| | - Bernard Lauwerys
- Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, Brussels, Belgium
- Department of Rheumatology, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Kyriacos Kyriacou
- Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Iroon Avenue 6, Agios Dometios, 2371, P.O. Box 23462 / 1683, Nicosia, Cyprus.
- Cyprus School of Molecular Medicine, Iroon Avenue 6, Agios Dometios, 2371, P.O. Box 23462 / 1683, Nicosia, Cyprus.
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