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Uzbas F, O’Neill AC. Spatial Centrosome Proteomic Profiling of Human iPSC-derived Neural Cells. Bio Protoc 2023; 13:e4812. [PMID: 37727868 PMCID: PMC10505934 DOI: 10.21769/bioprotoc.4812] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 06/05/2023] [Accepted: 06/12/2023] [Indexed: 09/21/2023] Open
Abstract
The centrosome governs many pan-cellular processes including cell division, migration, and cilium formation. However, very little is known about its cell type-specific protein composition and the sub-organellar domains where these protein interactions take place. Here, we outline a protocol for the spatial interrogation of the centrosome proteome in human cells, such as those differentiated from induced pluripotent stem cells (iPSCs), through co-immunoprecipitation of protein complexes around selected baits that are known to reside at different structural parts of the centrosome, followed by mass spectrometry. The protocol describes expansion and differentiation of human iPSCs to dorsal forebrain neural progenitors and cortical projection neurons, harvesting and lysis of cells for protein isolation, co-immunoprecipitation with antibodies against selected bait proteins, preparation for mass spectrometry, processing the mass spectrometry output files using MaxQuant software, and statistical analysis using Perseus software to identify the enriched proteins by each bait. Given the large number of cells needed for the isolation of centrosome proteins, this protocol can be scaled up or down by modifying the number of bait proteins and can also be carried out in batches. It can potentially be adapted for other cell types, organelles, and species as well.
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Affiliation(s)
- Fatma Uzbas
- Physiological Genomics, Biomedical Center (BMC), Ludwig-Maximilians-Universitaet (LMU), Planegg-Martinsried, Germany
- Institute of Stem Cell Research, Helmholtz Munich, German Research Center for Environmental Health, Planegg-Martinsried, Germany
| | - Adam C. O’Neill
- Physiological Genomics, Biomedical Center (BMC), Ludwig-Maximilians-Universitaet (LMU), Planegg-Martinsried, Germany
- Institute of Stem Cell Research, Helmholtz Munich, German Research Center for Environmental Health, Planegg-Martinsried, Germany
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Kyrousi C, O’Neill AC, Brazovskaja A, He Z, Kielkowski P, Coquand L, Di Giaimo R, D’ Andrea P, Belka A, Forero Echeverry A, Mei D, Lenge M, Cruceanu C, Buchsbaum IY, Khattak S, Fabien G, Binder E, Elmslie F, Guerrini R, Baffet AD, Sieber SA, Treutlein B, Robertson SP, Cappello S. Extracellular LGALS3BP regulates neural progenitor position and relates to human cortical complexity. Nat Commun 2021; 12:6298. [PMID: 34728600 PMCID: PMC8564519 DOI: 10.1038/s41467-021-26447-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 09/26/2021] [Indexed: 12/15/2022] Open
Abstract
Basal progenitors (BPs), including intermediate progenitors and basal radial glia, are generated from apical radial glia and are enriched in gyrencephalic species like humans, contributing to neuronal expansion. Shortly after generation, BPs delaminate towards the subventricular zone, where they further proliferate before differentiation. Gene expression alterations involved in BP delamination and function in humans are poorly understood. Here, we study the role of LGALS3BP, so far known as a cancer biomarker, which is a secreted protein enriched in human neural progenitors (NPCs). We show that individuals with LGALS3BP de novo variants exhibit altered local gyrification, sulcal depth, surface area and thickness in their cortex. Additionally, using cerebral organoids, human fetal tissues and mice, we show that LGALS3BP regulates the position of NPCs. Single-cell RNA-sequencing and proteomics reveal that LGALS3BP-mediated mechanisms involve the extracellular matrix in NPCs' anchoring and migration within the human brain. We propose that its temporal expression influences NPCs' delamination, corticogenesis and gyrification extrinsically.
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Affiliation(s)
- Christina Kyrousi
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, 80804 Munich, Germany ,grid.5216.00000 0001 2155 0800Present Address: First Department of Psychiatry, Medical School, National and Kapodistrian University of Athens, Greece and University Mental Health, Neurosciences and Precision Medicine Research Institute “Costas Stefanis”, Athens, Greece
| | - Adam C. O’Neill
- grid.29980.3a0000 0004 1936 7830Department of Women’s and Children’s Health, University of Otago, 9054 Dunedin, New Zealand
| | - Agnieska Brazovskaja
- grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Zhisong He
- grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany ,grid.5801.c0000 0001 2156 2780ETH Zurich, Department of Biosystems Science and Engineering, 4058 Basel, Switzerland
| | - Pavel Kielkowski
- grid.6936.a0000000123222966Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Garching, Germany ,grid.5252.00000 0004 1936 973XPresent Address: Department Chemie Ludwig-Maximilians-Universität München Butenandtstr. 5-13, 81377 München, Germany
| | - Laure Coquand
- grid.4444.00000 0001 2112 9282Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d’Ulm, F-75005 Paris, France
| | - Rossella Di Giaimo
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, 80804 Munich, Germany ,grid.4691.a0000 0001 0790 385XDepartment of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Pierpaolo D’ Andrea
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Alexander Belka
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | | | - Davide Mei
- grid.413181.e0000 0004 1757 8562Neuroscience Department, Children’s Hospital A. Meyer-University of Florence, 50139 Florence, Italy
| | - Matteo Lenge
- grid.413181.e0000 0004 1757 8562Neuroscience Department, Children’s Hospital A. Meyer-University of Florence, 50139 Florence, Italy
| | - Cristiana Cruceanu
- grid.419548.50000 0000 9497 5095Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Isabel Y. Buchsbaum
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, 80804 Munich, Germany ,grid.5252.00000 0004 1936 973XGraduate School of Systemic Neurosciences, Ludwig-Maximilians-University, 82152 Munich Planegg, Germany
| | - Shahryar Khattak
- grid.4488.00000 0001 2111 7257DFG-Research Center and Cluster of Excellence for Regenerative Therapies (CRTD), School of Medicine, Technical University Dresden, 01307 Dresden, Germany ,grid.4912.e0000 0004 0488 7120Present Address: Royal College of Surgeons Ireland (RCSI) in Bahrain, Adliya, Kingdom of Bahrain
| | - Guimiot Fabien
- grid.50550.350000 0001 2175 4109Unité de Foetopathologie, Assistance Publique-Hôpitaux de Paris, CHU Robert Debré, F-75019 Paris, France
| | - Elisabeth Binder
- grid.419548.50000 0000 9497 5095Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Frances Elmslie
- grid.4464.20000 0001 2161 2573South West Thames Regional Genetics Service, St George’s, University of London, London, SW17 0RE UK
| | - Renzo Guerrini
- grid.413181.e0000 0004 1757 8562Neuroscience Department, Children’s Hospital A. Meyer-University of Florence, 50139 Florence, Italy
| | - Alexandre D. Baffet
- grid.4444.00000 0001 2112 9282Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d’Ulm, F-75005 Paris, France
| | - Stephan A. Sieber
- grid.6936.a0000000123222966Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Garching, Germany
| | - Barbara Treutlein
- grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany ,grid.5801.c0000 0001 2156 2780ETH Zurich, Department of Biosystems Science and Engineering, 4058 Basel, Switzerland
| | - Stephen P. Robertson
- grid.29980.3a0000 0004 1936 7830Department of Women’s and Children’s Health, University of Otago, 9054 Dunedin, New Zealand
| | - Silvia Cappello
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, 80804 Munich, Germany
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Abstract
The ability to reprogram fully differentiated cells into a pluripotent embryonic state, termed induced pluripotent stem cells (iPSCs), has been met with great excitement. iPSC technology has advanced the fundamental study of disease modeling with the potential for cell-replacement therapy, especially in the neuronal and cardiac fields. However, renal medicine as of yet has not benefited from similar advancements. This review summarizes the unique characteristics of iPSCs and their potential applications for modeling kidney disease. Pioneering such endeavors could yield constructs that recapitulate disease phenotypes, open avenues for more targeted drug development, and potentially serve as replenishable sources for replacement of kidney cells in the setting of human disease.
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Affiliation(s)
- Adam C. O’Neill
- Department of Pediatrics, Dunedin School of Medicine, Otago University, Dunedin, New Zealand, and
| | - Sharon D. Ricardo
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
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