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Frank E, Cailleret M, Nelep C, Fragner P, Polentes J, Herardot E, El Kassar L, Giraud-Triboult K, Monville C, Ben M'Barek K. Semi-automated optimized method to isolate CRISPR/Cas9 edited human pluripotent stem cell clones. Stem Cell Res Ther 2023; 14:110. [PMID: 37106426 PMCID: PMC10142500 DOI: 10.1186/s13287-023-03327-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
BACKGROUND CRISPR/Cas9 editing systems are currently used to generate mutations in a particular gene to mimic a genetic disorder in vitro. Such "disease in a dish" models based on human pluripotent stem cells (hPSCs) offer the opportunity to have access to virtually all cell types of the human body. However, the generation of mutated hPSCs remains fastidious. Current CRISPR/Cas9 editing approaches lead to a mixed cell population containing simultaneously non-edited and a variety of edited cells. These edited hPSCs need therefore to be isolated through manual dilution cloning, which is time-consuming, labor intensive and tedious. METHODS Following CRISPR/Cas9 edition, we obtained a mixed cell population with various edited cells. We then used a semi-automated robotic platform to isolate single cell-derived clones. RESULTS We optimized CRISPR/Cas9 editing to knock out a representative gene and developed a semi-automated method for the clonal isolation of edited hPSCs. This method is faster and more reliable than current manual approaches. CONCLUSIONS This novel method of hPSC clonal isolation will greatly improve and upscale the generation of edited hPSCs required for downstream applications including disease modeling and drug screening.
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Affiliation(s)
- Elie Frank
- INSERM U861, I-Stem, AFM, Institute for Stem cell Therapy and Exploration of Monogenic Diseases, 91100, Corbeil-Essonnes, France
- U861, I-Stem, AFM, Université Paris-Saclay, Université d'Evry, 91100, Corbeil-Essonnes, France
| | - Michel Cailleret
- INSERM U861, I-Stem, AFM, Institute for Stem cell Therapy and Exploration of Monogenic Diseases, 91100, Corbeil-Essonnes, France
- U861, I-Stem, AFM, Université Paris-Saclay, Université d'Evry, 91100, Corbeil-Essonnes, France
| | | | - Pascal Fragner
- INSERM U861, I-Stem, AFM, Institute for Stem cell Therapy and Exploration of Monogenic Diseases, 91100, Corbeil-Essonnes, France
- U861, I-Stem, AFM, Université Paris-Saclay, Université d'Evry, 91100, Corbeil-Essonnes, France
- CECS, Centre d'étude des cellules souches, 91100, Corbeil-Essonnes, France
| | - Jérome Polentes
- INSERM U861, I-Stem, AFM, Institute for Stem cell Therapy and Exploration of Monogenic Diseases, 91100, Corbeil-Essonnes, France
- U861, I-Stem, AFM, Université Paris-Saclay, Université d'Evry, 91100, Corbeil-Essonnes, France
- CECS, Centre d'étude des cellules souches, 91100, Corbeil-Essonnes, France
| | - Elise Herardot
- INSERM U861, I-Stem, AFM, Institute for Stem cell Therapy and Exploration of Monogenic Diseases, 91100, Corbeil-Essonnes, France
- U861, I-Stem, AFM, Université Paris-Saclay, Université d'Evry, 91100, Corbeil-Essonnes, France
| | - Lina El Kassar
- INSERM U861, I-Stem, AFM, Institute for Stem cell Therapy and Exploration of Monogenic Diseases, 91100, Corbeil-Essonnes, France
- U861, I-Stem, AFM, Université Paris-Saclay, Université d'Evry, 91100, Corbeil-Essonnes, France
- CECS, Centre d'étude des cellules souches, 91100, Corbeil-Essonnes, France
| | - Karine Giraud-Triboult
- INSERM U861, I-Stem, AFM, Institute for Stem cell Therapy and Exploration of Monogenic Diseases, 91100, Corbeil-Essonnes, France
- U861, I-Stem, AFM, Université Paris-Saclay, Université d'Evry, 91100, Corbeil-Essonnes, France
- CECS, Centre d'étude des cellules souches, 91100, Corbeil-Essonnes, France
| | - Christelle Monville
- INSERM U861, I-Stem, AFM, Institute for Stem cell Therapy and Exploration of Monogenic Diseases, 91100, Corbeil-Essonnes, France.
- U861, I-Stem, AFM, Université Paris-Saclay, Université d'Evry, 91100, Corbeil-Essonnes, France.
| | - Karim Ben M'Barek
- INSERM U861, I-Stem, AFM, Institute for Stem cell Therapy and Exploration of Monogenic Diseases, 91100, Corbeil-Essonnes, France.
- U861, I-Stem, AFM, Université Paris-Saclay, Université d'Evry, 91100, Corbeil-Essonnes, France.
- CECS, Centre d'étude des cellules souches, 91100, Corbeil-Essonnes, France.
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Mérien A, Tahraoui-Bories J, Cailleret M, Dupont JB, Leteur C, Polentes J, Carteron A, Polvèche H, Concordet JP, Pinset C, Jarrige M, Furling D, Martinat C. CRISPR gene editing in pluripotent stem cells reveals the function of MBNL proteins during human in vitro myogenesis. Hum Mol Genet 2021; 31:41-56. [PMID: 34312665 PMCID: PMC8682758 DOI: 10.1093/hmg/ddab218] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/10/2021] [Accepted: 07/21/2021] [Indexed: 11/14/2022] Open
Abstract
Alternative splicing has emerged as a fundamental mechanism for the spatiotemporal control of development. A better understanding of how this mechanism is regulated has the potential not only to elucidate fundamental biological principles, but also to decipher pathological mechanisms implicated in diseases where normal splicing networks are misregulated. Here, we took advantage of human pluripotent stem cells to decipher during human myogenesis the role of muscleblind-like (MBNL) proteins, a family of tissue-specific splicing regulators whose loss of function is associated with myotonic dystrophy type 1 (DM1), an inherited neuromuscular disease. Thanks to the CRISPR/Cas9 technology, we generated human-induced pluripotent stem cells (hiPSCs) depleted in MBNL proteins and evaluated the consequences of their losses on the generation of skeletal muscle cells. Our results suggested that MBNL proteins are required for the late myogenic maturation. In addition, loss of MBNL1 and MBNL2 recapitulated the main features of DM1 observed in hiPSC-derived skeletal muscle cells. Comparative transcriptomic analyses also revealed the muscle-related processes regulated by these proteins that are commonly misregulated in DM1. Together, our study reveals the temporal requirement of MBNL proteins in human myogenesis and should facilitate the identification of new therapeutic strategies capable to cope with the loss of function of these MBNL proteins.
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Affiliation(s)
- Antoine Mérien
- INSERM/UEPS UMR 861, Paris Saclay University, I-STEM, 91100 Corbeil-Essonnes, France
| | - Julie Tahraoui-Bories
- INSERM/UEPS UMR 861, Paris Saclay University, I-STEM, 91100 Corbeil-Essonnes, France
| | - Michel Cailleret
- INSERM/UEPS UMR 861, Paris Saclay University, I-STEM, 91100 Corbeil-Essonnes, France
| | - Jean-Baptiste Dupont
- INSERM/UEPS UMR 861, Paris Saclay University, I-STEM, 91100 Corbeil-Essonnes, France
| | | | | | | | | | | | | | | | - Denis Furling
- Sorbonne Université, INSERM, Association Institut de Myologie, Centre de recherche en myologie, Paris, France
| | - Cécile Martinat
- INSERM/UEPS UMR 861, Paris Saclay University, I-STEM, 91100 Corbeil-Essonnes, France
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Araujo AN, Camacho CP, Mendes TB, Lindsey SC, Moraes L, Miyazawa M, Delcelo R, Pellegrino R, Mazzotti DR, Maciel RMDB, Cerutti JM. Comprehensive Assessment of Copy Number Alterations Uncovers Recurrent AIFM3 and DLK1 Copy Gain in Medullary Thyroid Carcinoma. Cancers (Basel) 2021; 13:cancers13020218. [PMID: 33435319 PMCID: PMC7826827 DOI: 10.3390/cancers13020218] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/03/2021] [Accepted: 01/05/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Medullary thyroid cancer (MTC) is often discovered in its advanced stage. Although a rare disease, advanced MTC cases have poor prognosis and the treatment is often palliative. Several studies have reported the existence of an association between copy number alterations (CNAs) burden and cancer progression. Moreover, the accumulation of broad CNAs, which contribute to intra-tumor heterogeneity, might be required for immune evasion. The identification of the recurrent CNAs associated with tumor phenotype aided in discovering new therapeutics options in several cancer types. To our knowledge, CNA is not well characterized in MTC. We analyzed recurrent focal CNAs on MTC. Our analysis provides a novel insight on MTC biology and may help in uncovering novel potential therapeutic targets. Abstract Medullary thyroid carcinoma (MTC) is a malignant tumor originating from thyroid C-cells that can occur either in sporadic (70–80%) or hereditary (20–30%) form. In this study we aimed to identify recurrent copy number alterations (CNA) that might be related to the pathogenesis or progression of MTC. We used Affymetrix SNP array 6.0 on MTC and paired-blood samples to identify CNA using PennCNV and Genotyping Console software. The algorithms identified recurrent copy number gains in chromosomes 15q, 10q, 14q and 22q in MTC, whereas 4q cumulated losses. Coding genes were identified within CNA regions. The quantitative PCR analysis performed in an independent series of MTCs (n = 51) confirmed focal recurrent copy number gains encompassing the DLK1 (14q32.2) and AIFM3 (22q11.21) genes. Immunohistochemistry confirmed AIFM3 and DLK1 expression in MTC cases, while no expression was found in normal thyroid tissues and few MTC samples were found with normal copy numbers. The functional relevance of CNA was also assessed by in silico analysis. CNA status correlated with protein expression (DLK1, p = 0.01), tumor size (DLK1, p = 0.04) and AJCC staging (AIFM3p = 0.01 and DLK1p = 0.05). These data provide a novel insight into MTC biology, and suggest a common CNA landscape, regardless of if it is sporadic or hereditary MTC.
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Affiliation(s)
- Aline Neves Araujo
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Pedro de Toledo 669, 11 andar, São Paulo 04039-032, Brazil; (A.N.A.); (T.B.M.); (L.M.); (M.M.)
| | - Cléber Pinto Camacho
- Laboratory of Molecular and Translational Endocrinology, Division of Endocrinology, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo, Pedro de Toledo 669, 11 andar, São Paulo 04039-032, Brazil; (C.P.C.); (S.C.L.); (R.M.d.B.M.)
| | - Thais Biude Mendes
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Pedro de Toledo 669, 11 andar, São Paulo 04039-032, Brazil; (A.N.A.); (T.B.M.); (L.M.); (M.M.)
| | - Susan Chow Lindsey
- Laboratory of Molecular and Translational Endocrinology, Division of Endocrinology, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo, Pedro de Toledo 669, 11 andar, São Paulo 04039-032, Brazil; (C.P.C.); (S.C.L.); (R.M.d.B.M.)
| | - Lais Moraes
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Pedro de Toledo 669, 11 andar, São Paulo 04039-032, Brazil; (A.N.A.); (T.B.M.); (L.M.); (M.M.)
| | - Marta Miyazawa
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Pedro de Toledo 669, 11 andar, São Paulo 04039-032, Brazil; (A.N.A.); (T.B.M.); (L.M.); (M.M.)
| | - Rosana Delcelo
- Department of Pathology, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Botucatu, 740, São Paulo 04023-900, Brazil;
| | - Renata Pellegrino
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Research Institute, 3401 Civic Center Blvd., Philadelphia, PA 191014, USA;
| | - Diego Robles Mazzotti
- Division of Sleep Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 191014, USA;
| | - Rui Monteiro de Barros Maciel
- Laboratory of Molecular and Translational Endocrinology, Division of Endocrinology, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo, Pedro de Toledo 669, 11 andar, São Paulo 04039-032, Brazil; (C.P.C.); (S.C.L.); (R.M.d.B.M.)
| | - Janete Maria Cerutti
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Pedro de Toledo 669, 11 andar, São Paulo 04039-032, Brazil; (A.N.A.); (T.B.M.); (L.M.); (M.M.)
- Correspondence: ; Tel.: +55-11-5576-4979
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