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van Gurp L, Fodoulian L, Oropeza D, Furuyama K, Bru-Tari E, Vu AN, Kaddis JS, Rodríguez I, Thorel F, Herrera PL. Generation of human islet cell type-specific identity genesets. Nat Commun 2022; 13:2020. [PMID: 35440614 PMCID: PMC9019032 DOI: 10.1038/s41467-022-29588-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/23/2022] [Indexed: 12/23/2022] Open
Abstract
Generation of surrogate cells with stable functional identities is crucial for developing cell-based therapies. Efforts to produce insulin-secreting replacement cells to treat diabetes require reliable tools to assess islet cellular identity. Here, we conduct a thorough single-cell transcriptomics meta-analysis to identify robustly expressed markers used to build genesets describing the identity of human α-, β-, γ- and δ-cells. These genesets define islet cellular identities better than previously published genesets. We show their efficacy to outline cell identity changes and unravel some of their underlying genetic mechanisms, whether during embryonic pancreas development or in experimental setups aiming at developing glucose-responsive insulin-secreting cells, such as pluripotent stem-cell differentiation or in adult islet cell reprogramming protocols. These islet cell type-specific genesets represent valuable tools that accurately benchmark gain and loss in islet cell identity traits.
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Affiliation(s)
- Léon van Gurp
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Leon Fodoulian
- Department of Genetics and Evolution, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211, Geneva, Switzerland
| | - Daniel Oropeza
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Kenichiro Furuyama
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, rue Michel-Servet 1, 1211, Geneva, Switzerland
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Shogoin-Kawahara, Sakyo, 606-8507, Kyoto, Japan
| | - Eva Bru-Tari
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Anh Nguyet Vu
- Department of Diabetes & Cancer Discovery Science, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, 1500 E Duarte Rd, Duarte, CA, 91010, USA
| | - John S Kaddis
- Department of Diabetes & Cancer Discovery Science, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, 1500 E Duarte Rd, Duarte, CA, 91010, USA
| | - Iván Rodríguez
- Department of Genetics and Evolution, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211, Geneva, Switzerland
| | - Fabrizio Thorel
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Pedro L Herrera
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, rue Michel-Servet 1, 1211, Geneva, Switzerland.
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