1
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Al Delbany D, Ghosh MS, Krivec N, Huyghebaert A, Regin M, Duong MC, Lei Y, Sermon K, Olsen C, Spits C. De Novo Cancer Mutations Frequently Associate with Recurrent Chromosomal Abnormalities during Long-Term Human Pluripotent Stem Cell Culture. Cells 2024; 13:1395. [PMID: 39195283 DOI: 10.3390/cells13161395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 08/16/2024] [Accepted: 08/20/2024] [Indexed: 08/29/2024] Open
Abstract
Human pluripotent stem cells (hPSCs) are pivotal in regenerative medicine, yet their in vitro expansion often leads to genetic abnormalities, raising concerns about their safety in clinical applications. This study analyzed ten human embryonic stem cell lines across multiple passages to elucidate the dynamics of chromosomal abnormalities and single-nucleotide variants (SNVs) in 380 cancer-related genes. Prolonged in vitro culture resulted in 80% of the lines acquiring gains of chromosome 20q or 1q, both known for conferring an in vitro growth advantage. 70% of lines also acquired other copy number variants (CNVs) outside the recurrent set. Additionally, we detected 122 SNVs in 88 genes, with all lines acquiring at least one de novo SNV during culture. Our findings showed higher loads of both CNVs and SNVs at later passages, which were due to the cumulative acquisition of mutations over a longer time in culture, and not to an increased rate of mutagenesis over time. Importantly, we observed that SNVs and rare CNVs followed the acquisition of chromosomal gains in 1q and 20q, while most of the low-passage and genetically balanced samples were devoid of cancer-associated mutations. This suggests that recurrent chromosomal abnormalities are potential drivers for the acquisition of other mutations.
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Affiliation(s)
- Diana Al Delbany
- Research Group Genetics, Reproduction and Development, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium
| | - Manjusha S Ghosh
- Research Group Genetics, Reproduction and Development, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium
| | - Nuša Krivec
- Research Group Genetics, Reproduction and Development, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium
| | - Anfien Huyghebaert
- Research Group Genetics, Reproduction and Development, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium
| | - Marius Regin
- Research Group Genetics, Reproduction and Development, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium
| | - Mai Chi Duong
- Research Group Genetics, Reproduction and Development, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium
- Department of Biochemistry, Military Hospital 175, 786 Nguyen Kiem Street, Ho Chi Minh City 71409, Vietnam
| | - Yingnan Lei
- Research Group Genetics, Reproduction and Development, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium
| | - Karen Sermon
- Research Group Genetics, Reproduction and Development, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium
| | - Catharina Olsen
- Research Group Genetics, Reproduction and Development, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium
- Brussels Interuniversity Genomics High Throughput Core (BRIGHTcore), Vrije Universiteit Brussel (VUB)-Université Libre de Bruxelles (ULB), Laarbeeklaan 101, 1090 Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles (ULB)-Vrije Universiteit Brussel (VUB), La Plaine Campus Triomflaan, 1050 Brussels, Belgium
| | - Claudia Spits
- Research Group Genetics, Reproduction and Development, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium
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2
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Militaru MS, Babliuc IM, Bloaje-Florică VL, Danci VA, Filip-Deac I, Kutasi E, Simon V, Militaru M, Cătană A. The Impact of Chromosomal Mosaicisms on Prenatal Diagnosis and Genetic Counseling-A Narrative Review. J Pers Med 2024; 14:774. [PMID: 39064028 PMCID: PMC11277968 DOI: 10.3390/jpm14070774] [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: 06/14/2024] [Revised: 07/13/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
Genetic disorders represent a high-impact diagnosis for both patients and their families. Prenatal screening methods and, when recommended, genetic testing allow parents to make informed decisions about the course a pregnancy is going to take. Although offering certainty about the potential evolution and prognosis of the pregnancy, and then the newborn, is usually not possible, genetic counseling can offer valuable insights into genetic disorders. Chromosomal mosaicisms are genetic anomalies that affect only some cell lines in either the fetus or the placenta or both. They can affect autosomal or heterosomal chromosomes, and they can be either numerical or structural. The prognosis seems to be more severe if the genetic alterations are accompanied by malformations visible in ultrasounds. Several genetic techniques can be used to diagnose certain mosaicisms, depending on their nature. A novel approach in prenatal care is non-invasive prenatal screening (NIPS), also known as non-invasive prenatal testing (NIPT), which, although it does not always have diagnostic value, can provide valuable information about potential genetic anomalies, especially numerical, with high sensitivity (Se).
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Affiliation(s)
- Mariela Sanda Militaru
- Department of Molecular Sciences, Faculty of Medicine, University of Medicine and Pharmacy “Iuliu Hatieganu”, 400012 Cluj-Napoca, Romania; (M.S.M.); (A.C.)
- Regional Laboratory Cluj-Napoca, Department of Medical Genetics, Regina Maria Health Network, 400363 Cluj-Napoca, Romania
| | - Ioana-Mădălina Babliuc
- Department for Mother and Child Health, Pediatric 1, Emergency County Hospital, No. 68 Motilor Street, 400394 Cluj-Napoca, Romania; (I.-M.B.); (V.-A.D.); (V.S.)
| | | | - Valentin-Adrian Danci
- Department for Mother and Child Health, Pediatric 1, Emergency County Hospital, No. 68 Motilor Street, 400394 Cluj-Napoca, Romania; (I.-M.B.); (V.-A.D.); (V.S.)
| | - Iulia Filip-Deac
- County Emergency Clinical Hospital, 50 Dr. Gheorghe Marinescu Street, 540136 Târgu Mureș, Romania;
| | - Enikő Kutasi
- Department of Molecular Sciences, Faculty of Medicine, University of Medicine and Pharmacy “Iuliu Hatieganu”, 400012 Cluj-Napoca, Romania; (M.S.M.); (A.C.)
- Department for Mother and Child Health, Pediatric 1, Emergency County Hospital, No. 68 Motilor Street, 400394 Cluj-Napoca, Romania; (I.-M.B.); (V.-A.D.); (V.S.)
| | - Vasile Simon
- Department for Mother and Child Health, Pediatric 1, Emergency County Hospital, No. 68 Motilor Street, 400394 Cluj-Napoca, Romania; (I.-M.B.); (V.-A.D.); (V.S.)
- Department of Urology, University of Medicine and Pharmacy “Iuliu Hatieganu”, 11 Tăbăcarilor Street, 400139 Cluj-Napoca, Romania
| | - Mihai Militaru
- Pediatric 2 Discipline, University of Medicine and Pharmacy “Iuliu Hatieganu”, Emergency County Hospital, No. 3-5 Clinicilor Street, 400535 Cluj-Napoca, Romania;
| | - Andreea Cătană
- Department of Molecular Sciences, Faculty of Medicine, University of Medicine and Pharmacy “Iuliu Hatieganu”, 400012 Cluj-Napoca, Romania; (M.S.M.); (A.C.)
- Regional Laboratory Cluj-Napoca, Department of Medical Genetics, Regina Maria Health Network, 400363 Cluj-Napoca, Romania
- Department of Oncogenetics, Institute of Oncology, “Prof. Dr. I. Chiricuță”, 400015 Cluj-Napoca, Romania
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3
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Lei Y, Al Delbany D, Krivec N, Regin M, Couvreu de Deckersberg E, Janssens C, Ghosh M, Sermon K, Spits C. SALL3 mediates the loss of neuroectodermal differentiation potential in human embryonic stem cells with chromosome 18q loss. Stem Cell Reports 2024; 19:562-578. [PMID: 38552632 PMCID: PMC11096619 DOI: 10.1016/j.stemcr.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 04/12/2024] Open
Abstract
Human pluripotent stem cell (hPSC) cultures are prone to genetic drift, because cells that have acquired specific genetic abnormalities experience a selective advantage in vitro. These abnormalities are highly recurrent in hPSC lines worldwide, but their functional consequences in differentiating cells are scarcely described. In this work, we show that the loss of chromosome 18q impairs neuroectoderm commitment and that downregulation of SALL3, a gene located in the common 18q loss region, is responsible for this failed neuroectodermal differentiation. Knockdown of SALL3 in control lines impaired differentiation in a manner similar to the loss of 18q, and transgenic overexpression of SALL3 in hESCs with 18q loss rescued the differentiation capacity of the cells. Finally, we show that loss of 18q and downregulation of SALL3 leads to changes in the expression of genes involved in pathways regulating pluripotency and differentiation, suggesting that these cells are in an altered state of pluripotency.
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Affiliation(s)
- Yingnan Lei
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Diana Al Delbany
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Nuša Krivec
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Marius Regin
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Edouard Couvreu de Deckersberg
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Charlotte Janssens
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Manjusha Ghosh
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Karen Sermon
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Claudia Spits
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium.
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Krivec N, Ghosh MS, Spits C. Gains of 20q11.21 in human pluripotent stem cells: Insights from cancer research. Stem Cell Reports 2024; 19:11-27. [PMID: 38157850 PMCID: PMC10828824 DOI: 10.1016/j.stemcr.2023.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/28/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024] Open
Abstract
The genetic abnormalities observed in hPSC cultures worldwide have been suggested to pose an important hurdle in their safe use in regenerative medicine due to the possibility of oncogenic transformation by mutant cells in the patient posttransplantation. One of the best-characterized genetic lesions in hPSCs is the gain of 20q11.21, found in 20% of hPSC lines worldwide, and strikingly, also amplified in 20% of human cancers. In this review, we have curated the existing knowledge on the incidence of this mutation in hPSCs and cancer, explored the significance of chromosome 20q11.21 amplification in cancer progression, and reviewed the oncogenic role of the genes in the smallest common region of gain, to shed light on the significance of this mutation in hPSC-based cell therapy. Lastly, we discuss the state-of-the-art strategies devised to detect aneuploidies in hPSC cultures, avoid genetic changes in vitro cultures of hPSCs, and strategies to eliminate genetically abnormal cells from culture.
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Affiliation(s)
- Nuša Krivec
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Manjusha S Ghosh
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Claudia Spits
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium.
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5
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Solís-Moruno M, Batlle-Masó L, Bonet N, Aróstegui JI, Casals F. Somatic genetic variation in healthy tissue and non-cancer diseases. Eur J Hum Genet 2023; 31:48-54. [PMID: 36289407 PMCID: PMC9823099 DOI: 10.1038/s41431-022-01213-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 09/19/2022] [Accepted: 10/03/2022] [Indexed: 02/08/2023] Open
Abstract
Somatic genetic variants have been studied for several years mostly concerning cancer, where they contribute to its origin and development. It is also clear that the somatic variants load is greater in aged individuals in comparison to younger ones, pointing to a cause/consequence of the senescence process. More recently, researchers have focused on the role of this type of variation in healthy tissue and its dynamics in cell lineages and different organs. In addition, somatic variants have been described to contribute to monogenic diseases, and the number of evidences of their role in complex disorders is also increasing. Thanks to recent advances in next-generation sequencing technologies, this type of genetic variation can be now more easily studied than in the past, although we still face some important limitations. Novel strategies for sampling, sequencing and filtering are being investigated to detect these variants, although validating them with an orthogonal approach will most likely still be needed. In this review, we aim to update our knowledge of somatic variation detection and its relation to healthy tissue and non-cancer diseases.
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Affiliation(s)
- Manuel Solís-Moruno
- grid.5612.00000 0001 2172 2676Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, Spain ,grid.5612.00000 0001 2172 2676Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Spain ,grid.410458.c0000 0000 9635 9413Department of Immunology, Hospital Clínic, Barcelona, Spain ,grid.10403.360000000091771775Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Laura Batlle-Masó
- grid.7080.f0000 0001 2296 0625Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d’Hebron (HUVH), Vall d’Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Núria Bonet
- grid.5612.00000 0001 2172 2676Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Spain
| | - Juan I. Aróstegui
- grid.410458.c0000 0000 9635 9413Department of Immunology, Hospital Clínic, Barcelona, Spain ,grid.10403.360000000091771775Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain ,grid.5841.80000 0004 1937 0247Universitat de Barcelona, Barcelona, Spain
| | - Ferran Casals
- grid.5612.00000 0001 2172 2676Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Spain ,grid.5841.80000 0004 1937 0247Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain ,grid.5841.80000 0004 1937 0247Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona, Spain
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6
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Hu B, Gong Y, Wang Y, Xie J, Cheng J, Huang Q. Comprehensive Atlas of Circulating Rare Cells Detected by SE-iFISH and Image Scanning Platform in Patients With Various Diseases. Front Oncol 2022; 12:821454. [PMID: 35311070 PMCID: PMC8924462 DOI: 10.3389/fonc.2022.821454] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/07/2022] [Indexed: 12/23/2022] Open
Abstract
Objective Circulating rare cells (CRCs) are known as a crucial nucleated cellular response to pathological conditions, yet the landscape of cell types across a wide variety of diseases lacks comprehensive understanding. This study aimed at detecting and presenting a full spectrum of highly heterogeneous CRCs in clinical practice and further explored the characterization of CRC subtypes in distinct biomarker combinations and aneuploid chromosomes among various disease groups. Methods Peripheral blood was obtained from 2,360 patients with different cancers and non-neoplastic diseases. CRC capture and identification were accomplished using a novel platform integrating subtraction enrichment and immunostaining-fluorescence in situ hybridization (SE-iFISH) strategy with a high-throughput automated image scanning system, on which hemocyte, tumor, epithelial, endothelial, mesenchymal, and stemness biomarkers were immunostained and displayed simultaneously. Double chromosome enumeration probe (CEP8 and CEP12) co-detection was performed on isolated CRCs from an extended trial for two chromosome ploidy patterns. Results A comprehensive atlas categorizing the diverse CRCs into 71 subtypes outlining was mapped out. The presence of epithelial-mesenchymal transition (EMT) or endothelial-mesenchymal transition (EndoMT), the cells with progenitor property, hematologic CRCs expressing multiple biomarkers, CRCs at "naked nuclei" status, and the rarely reported aneuploid mesenchymal epithelial-endothelial fusion cluster were described. Circulating tumor cells (CTCs) were detected in 2,157 (91.4%) patients; the total numbers of CTCs and circulating tumor-derived endothelial cells (CTECs) were relatively higher in several digestive system cancer types and non-neoplastic infectious diseases (p < 0.05). Co-detection combining CEP8 and CEP12 showed a higher diagnostic specificity on account of 57.27% false negativity of CRC detection through a single probe of CEP8. Conclusions The alternative biomarkers and chromosomes to be targeted by SE-iFISH and the image scanning platform, along with the comprehensive atlas, offer insight into the heterogeneity of CRCs and reveal potential contributions to specific disease diagnosis and therapeutic target cell discovery.
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Affiliation(s)
- Binjie Hu
- Molecular Diagnostics Laboratory of Cancer Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanping Gong
- Molecular Diagnostics Laboratory of Cancer Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yulan Wang
- Molecular Diagnostics Laboratory of Cancer Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianzhu Xie
- Molecular Diagnostics Laboratory of Cancer Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jin Cheng
- Molecular Diagnostics Laboratory of Cancer Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qian Huang
- Molecular Diagnostics Laboratory of Cancer Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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7
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Keller A, Spits C. The Impact of Acquired Genetic Abnormalities on the Clinical Translation of Human Pluripotent Stem Cells. Cells 2021; 10:cells10113246. [PMID: 34831467 PMCID: PMC8625075 DOI: 10.3390/cells10113246] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/07/2021] [Accepted: 11/17/2021] [Indexed: 12/23/2022] Open
Abstract
Human pluripotent stem cells (hPSC) are known to acquire chromosomal abnormalities, which range from point mutations to large copy number changes, including full chromosome aneuploidy. These aberrations have a wide-ranging influence on the state of cells, in both the undifferentiated and differentiated state. Currently, very little is known on how these abnormalities will impact the clinical translation of hPSC, and particularly their potential to prime cells for oncogenic transformation. A further complication is that many of these abnormalities exist in a mosaic state in culture, which complicates their detection with conventional karyotyping methods. In this review we discuss current knowledge on how these aberrations influence the cell state and how this may impact the future of research and the cells’ clinical potential.
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Dziedzicka D, Tewary M, Keller A, Tilleman L, Prochazka L, Östblom J, Couvreu De Deckersberg E, Markouli C, Franck S, Van Nieuwerburgh F, Spits C, Zandstra PW, Sermon K, Geens M. Endogenous suppression of WNT signalling in human embryonic stem cells leads to low differentiation propensity towards definitive endoderm. Sci Rep 2021; 11:6137. [PMID: 33731744 PMCID: PMC7969605 DOI: 10.1038/s41598-021-85447-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/23/2021] [Indexed: 02/06/2023] Open
Abstract
Low differentiation propensity towards a targeted lineage can significantly hamper the utility of individual human pluripotent stem cell (hPSC) lines in biomedical applications. Here, we use monolayer and micropatterned cell cultures, as well as transcriptomic profiling, to investigate how variability in signalling pathway activity between human embryonic stem cell lines affects their differentiation efficiency towards definitive endoderm (DE). We show that endogenous suppression of WNT signalling in hPSCs at the onset of differentiation prevents the switch from self-renewal to DE specification. Gene expression profiling reveals that this inefficient switch is reflected in NANOG expression dynamics. Importantly, we demonstrate that higher WNT stimulation or inhibition of the PI3K/AKT signalling can overcome the DE commitment blockage. Our findings highlight that redirection of the activity of Activin/NODAL pathway by WNT signalling towards mediating DE fate specification is a vulnerable spot, as disruption of this process can result in poor hPSC specification towards DE.
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Affiliation(s)
- Dominika Dziedzicka
- grid.8767.e0000 0001 2290 8069Research Group Reproduction and Genetics, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Mukul Tewary
- grid.17063.330000 0001 2157 2938Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3E1 Canada ,grid.13097.3c0000 0001 2322 6764Centre for Stem Cells and Regenerative Medicine, King’s College London, Guy’s Hospital, London, SE1 9RT UK
| | - Alexander Keller
- grid.8767.e0000 0001 2290 8069Research Group Reproduction and Genetics, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Laurentijn Tilleman
- grid.5342.00000 0001 2069 7798Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Laura Prochazka
- grid.17063.330000 0001 2157 2938Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3E1 Canada
| | - Joel Östblom
- grid.17063.330000 0001 2157 2938Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3E1 Canada
| | - Edouard Couvreu De Deckersberg
- grid.8767.e0000 0001 2290 8069Research Group Reproduction and Genetics, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Christina Markouli
- grid.8767.e0000 0001 2290 8069Research Group Reproduction and Genetics, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Silvie Franck
- grid.8767.e0000 0001 2290 8069Research Group Reproduction and Genetics, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Filip Van Nieuwerburgh
- grid.5342.00000 0001 2069 7798Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Claudia Spits
- grid.8767.e0000 0001 2290 8069Research Group Reproduction and Genetics, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Peter W. Zandstra
- grid.17063.330000 0001 2157 2938Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3E1 Canada ,grid.17091.3e0000 0001 2288 9830Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4 Canada ,grid.17091.3e0000 0001 2288 9830School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z3 Canada
| | - Karen Sermon
- grid.8767.e0000 0001 2290 8069Research Group Reproduction and Genetics, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Mieke Geens
- grid.8767.e0000 0001 2290 8069Research Group Reproduction and Genetics, Vrije Universiteit Brussel, 1090 Brussels, Belgium
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9
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Madian A, Eid MM, Shahin AAB, Mazen I, El-Bassyouni HT, Eid OM. Detection of low-grade mosaicism and its correlation with hormonal profile, testicular volume, and semen quality in a cohort of Egyptian Klinefelter and Klinefelter-like patients. Reprod Biol 2020; 20:259-263. [PMID: 32115387 DOI: 10.1016/j.repbio.2020.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 02/05/2020] [Accepted: 02/14/2020] [Indexed: 11/18/2022]
Abstract
Klinefelter syndrome (KS) is the most common chromosomal syndrome, causing infertility in men and leading to non-obstructive azoospermia. Previous studies on mosaicism have shown contradictory results on its correlation with both serum hormone levels and the presence of spermatozoa in the ejaculate of KS, KS-like, and non-KS-like infertile patients. So, the present study was designed to detect low-grade mosaicism in the peripheral blood lymphocytes and buccal mucosa cells of 14 KS and 8 KS-like patients by using fluorescence in situ hybridization (FISH) and to investigate its correlation with luteinizing hormone (LH), follicle-stimulating hormone (FSH), and testosterone (T) levels, testicular volume, and semen analysis compared with 10 normal healthy fertile men. Our results indicated that mosaicism was only found in 42.9 % of the KS patients and completely absent in all KS-like patients. Moreover, mosaicism has led to complete azoospermia and non-significant differences in both hormone levels and testicular volume between mosaic and non-mosaic KS patients. All KS patients demonstrated significant differences in both hormone levels and testicular volume compared with normal men. Conversely, they revealed non-significant differences in hormone levels and significant differences in testicular volume compared with KS-like patients. Additionally, the KS-like patients exhibited non-significant variations in both LH and FSH levels and significant variations in T level and testicular volume compared with normal men. Moreover, all KS-like patients had azoospermia, except for one patient who showed oligozoospermia. Therefore, no correlations were found either between mosaicism and serum hormone levels or with testicular volume and semen analysis.
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Affiliation(s)
| | - Maha M Eid
- Human Cytogenetics, National Research Center, 12622, Cairo, Egypt
| | - Adel A B Shahin
- Department of Zoology, Faculty of Science, Minia University, 61519, El Minia, Egypt.
| | - Inas Mazen
- Department of Clinical Genetics, National Research Center, 12622, Cairo, Egypt
| | - Hala T El-Bassyouni
- Department of Clinical Genetics, National Research Center, 12622, Cairo, Egypt
| | - Ola M Eid
- Human Cytogenetics, National Research Center, 12622, Cairo, Egypt
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10
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Uncovering low-level mosaicism in human embryonic stem cells using high throughput single cell shallow sequencing. Sci Rep 2019; 9:14844. [PMID: 31619727 PMCID: PMC6796059 DOI: 10.1038/s41598-019-51314-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 09/25/2019] [Indexed: 01/05/2023] Open
Abstract
Human pluripotent stem cells (hPSCs) have significant levels of low-grade genetic mosaicism, which commonly used techniques fail to detect in bulk DNA. These copy number variations remain a hurdle for the clinical translation of hPSC, as their effect in vivo ranges from unknown to dangerous, and the ability to detect them will be necessary as the field advances. As such there is need for techniques which can efficiently analyse genetic content in single cells with higher throughput and lower costs. We report here on the use of the Fluidigm C1 single cell WGA platform in combination with shallow whole genome sequencing to analyse the genetic content of single hPSCs. From a hPSC line carrying an isochromosome 20, 56 single cells were analysed and found to carry a total of 50 aberrations, across 23% of cells, which could not be detected by bulk analysis. Aberrations were predominantly segmental gains, with a fewer number of segmental losses and aneuploidies. Interestingly, 40% of the breakpoints seen here correspond to known DNA fragile sites. Our results therefore demonstrate the feasibility of single cell shallow sequencing of hPSC and further expand upon the biological importance and frequency of single cell mosaicism in hPSC.
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11
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Raghuram GV, Chaudhary S, Johari S, Mittra I. Illegitimate and Repeated Genomic Integration of Cell-Free Chromatin in the Aetiology of Somatic Mosaicism, Ageing, Chronic Diseases and Cancer. Genes (Basel) 2019; 10:genes10060407. [PMID: 31142004 PMCID: PMC6628102 DOI: 10.3390/genes10060407] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/15/2019] [Accepted: 05/22/2019] [Indexed: 12/19/2022] Open
Abstract
Emerging evidence suggests that an individual is a complex mosaic of genetically divergent cells. Post-zygotic genomes of the same individual can differ from one another in the form of single nucleotide variations, copy number variations, insertions, deletions, inversions, translocations, other structural and chromosomal variations and footprints of transposable elements. High-throughput sequencing has led to increasing detection of mosaicism in healthy individuals which is related to ageing, neuro-degenerative disorders, diabetes mellitus, cardiovascular diseases and cancer. These age-related disorders are also known to be associated with significant increase in DNA damage and inflammation. Herein, we discuss a newly described phenomenon wherein the genome is under constant assault by illegitimate integration of cell-free chromatin (cfCh) particles that are released from the billions of cells that die in the body every day. We propose that such repeated genomic integration of cfCh followed by dsDNA breaks and repair by non-homologous-end-joining as well as physical damage to chromosomes occurring throughout life may lead to somatic/chromosomal mosaicism which would increase with age. We also discuss the recent finding that genomic integration of cfCh and the accompanying DNA damage is associated with marked activation of inflammatory cytokines. Thus, the triple pathologies of somatic mosaicism, DNA/chromosomal damage and inflammation brought about by a common mechanism of genomic integration of cfCh may help to provide an unifying model for the understanding of aetiologies of the inter-related conditions of ageing, degenerative disorders and cancer.
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Affiliation(s)
- Gorantla V Raghuram
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai 410210, India.
| | - Shahid Chaudhary
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai 410210, India.
| | - Shweta Johari
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai 410210, India.
| | - Indraneel Mittra
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai 410210, India.
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Addressing Variability and Heterogeneity of Induced Pluripotent Stem Cell-Derived Cardiomyocytes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1212:1-29. [DOI: 10.1007/5584_2019_350] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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13
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Mishra S, Kacin E, Stamatiadis P, Franck S, Van der Jeught M, Mertes H, Pennings G, De Sutter P, Sermon K, Heindryckx B, Geens M. The role of the reprogramming method and pluripotency state in gamete differentiation from patient-specific human pluripotent stem cells. Mol Hum Reprod 2019; 24:173-184. [PMID: 29471503 DOI: 10.1093/molehr/gay007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 02/10/2018] [Indexed: 12/16/2022] Open
Abstract
The derivation of gametes from patient-specific pluripotent stem cells may provide new perspectives for genetic parenthood for patients currently facing sterility. We use current data to assess the gamete differentiation potential of patient-specific pluripotent stem cells and to determine which reprogramming strategy holds the greatest promise for future clinical applications. First, we compare the two best established somatic cell reprogramming strategies: the production of induced pluripotent stem cells (iPSC) and somatic cell nuclear transfer followed by embryonic stem cell derivation (SCNT-ESC). Recent reports have indicated that these stem cells, though displaying a similar pluripotency potential, show important differences at the epigenomic level, which may have repercussions on their applicability. By comparing data on the genetic and epigenetic stability of these cell types during derivation and in-vitro culture, we assess the reprogramming efficiency of both technologies and possible effects on the subsequent differentiation potential of these cells. Moreover, we discuss possible implications of mitochondrial heteroplasmy. We also address the ethical aspects of both cell types, as well as the safety considerations associated with clinical applications using these cells, e.g. the known genomic instability of human PSCs during long-term culture. Secondly, we discuss the role of the stem cell pluripotency state in germ cell differentiation. In mice, success in germ cell development from pluripotent stem cells could only be achieved when starting from a naive state of pluripotency. It remains to be investigated if the naive state is also crucial for germ cell differentiation in human cells and to what extent human naive pluripotency resembles the naive state in mouse.
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Affiliation(s)
- S Mishra
- Ghent-Fertility and Stem Cell Team, Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - E Kacin
- Research Group, Reproduction and Genetics, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Brussels, Belgium
| | - P Stamatiadis
- Ghent-Fertility and Stem Cell Team, Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - S Franck
- Research Group, Reproduction and Genetics, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Brussels, Belgium
| | - M Van der Jeught
- Ghent-Fertility and Stem Cell Team, Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - H Mertes
- Bioethics Institute Ghent, Department of Philosophy and Moral Sciences, Blandijnberg 2, 9000 Ghent, Belgium
| | - G Pennings
- Bioethics Institute Ghent, Department of Philosophy and Moral Sciences, Blandijnberg 2, 9000 Ghent, Belgium
| | - P De Sutter
- Ghent-Fertility and Stem Cell Team, Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - K Sermon
- Research Group, Reproduction and Genetics, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Brussels, Belgium
| | - B Heindryckx
- Ghent-Fertility and Stem Cell Team, Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - M Geens
- Research Group, Reproduction and Genetics, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Brussels, Belgium
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14
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Zambelli F, Mertens J, Dziedzicka D, Sterckx J, Markouli C, Keller A, Tropel P, Jung L, Viville S, Van de Velde H, Geens M, Seneca S, Sermon K, Spits C. Random Mutagenesis, Clonal Events, and Embryonic or Somatic Origin Determine the mtDNA Variant Type and Load in Human Pluripotent Stem Cells. Stem Cell Reports 2018; 11:102-114. [PMID: 29910126 PMCID: PMC6117474 DOI: 10.1016/j.stemcr.2018.05.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 05/10/2018] [Accepted: 05/15/2018] [Indexed: 01/13/2023] Open
Abstract
In this study, we deep-sequenced the mtDNA of human embryonic and induced pluripotent stem cells (hESCs and hiPSCs) and their source cells and found that the majority of variants pre-existed in the cells used to establish the lines. Early-passage hESCs carried few and low-load heteroplasmic variants, similar to those identified in oocytes and inner cell masses. The number and heteroplasmic loads of these variants increased with prolonged cell culture. The study of 120 individual cells of early- and late-passage hESCs revealed a significant diversity in mtDNA heteroplasmic variants at the single-cell level and that the variants that increase during time in culture are always passenger to the appearance of chromosomal abnormalities. We found that early-passage hiPSCs carry much higher loads of mtDNA variants than hESCs, which single-fibroblast sequencing proved pre-existed in the source cells. Finally, we show that these variants are stably transmitted during short-term differentiation.
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Affiliation(s)
- Filippo Zambelli
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, Brussels 1090, Belgium; S.I.S.Me.R. Reproductive Medicine Unit, Via Mazzini 12, Bologna 40100, Italy
| | - Joke Mertens
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, Brussels 1090, Belgium
| | - Dominika Dziedzicka
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, Brussels 1090, Belgium
| | - Johan Sterckx
- Centre for Reproductive Medicine, Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, Brussels, Belgium
| | - Christina Markouli
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, Brussels 1090, Belgium
| | - Alexander Keller
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, Brussels 1090, Belgium
| | | | - Laura Jung
- Institut de Parasitologie et Pathologie Tropicale, EA 7292, Fédérationde Médecine Translationelle, Université de Strasbourg, 3 rue Koeberlé, Strasbourg 67000, France
| | - Stephane Viville
- Institut de Parasitologie et Pathologie Tropicale, EA 7292, Fédérationde Médecine Translationelle, Université de Strasbourg, 3 rue Koeberlé, Strasbourg 67000, France; Laboratoire de Diagnostic Génétique, UF3472-génétique de l'infertilité, Hôpitaux Universitaires de Strasbourg, Strasbourg 67000, France
| | - Hilde Van de Velde
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, Brussels 1090, Belgium; Centre for Reproductive Medicine, Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, Brussels, Belgium
| | - Mieke Geens
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, Brussels 1090, Belgium
| | - Sara Seneca
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, Brussels 1090, Belgium; Centre for Medical Genetics, UZ Brussel, Laarbeeklaan 101, Brussels, Belgium
| | - Karen Sermon
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, Brussels 1090, Belgium
| | - Claudia Spits
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, Brussels 1090, Belgium.
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15
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Capalbo A, Ubaldi FM, Rienzi L, Scott R, Treff N. Detecting mosaicism in trophectoderm biopsies: current challenges and future possibilities. Hum Reprod 2018; 32:492-498. [PMID: 27738115 PMCID: PMC5400043 DOI: 10.1093/humrep/dew250] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 09/12/2016] [Indexed: 01/07/2023] Open
Abstract
Embryonic mosaicism, defined as the presence of karyotypically distinct cell lines within an embryo, has been frequently reported with a high incidence in preimplantation embryos derived from IVF and is thought to be one of the major biological limitations for the routine application of PGD for aneuploidies (PGD-A). The incidence of mosaicism in preimplantation embryos is in fact reported to be between 4 and 90%. However, these data are in sharp contrast with what is known from clinical pregnancies, where true foetal mosaicism is observed in less than 0.5% of cases. Here, we challenge these previous observations in preimplantation embryos, presenting an alternative perspective, which also considers the impact of technical variation to diagnose mosaicism as one possible cause contributing to overestimation of the incidence of mosaicism in embryos. Although euploid/aneuploid mosaicism may be present in blastocysts, the possibility of detecting this phenomenon within a single trophectoderm biopsy represents a contemporary challenge to bring about improvement to the practice of PGD-A. The purpose of this opinion paper is to provide a critical review of the literature, provide a possible alternative interpretation of the data, and discuss future challenges with diagnosing mosaicism in PGD-A cycles.
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Affiliation(s)
- Antonio Capalbo
- GENERA, Centers for Reproductive Medicine, Via G. De Notaris 2/B, Rome 00197, Italy.,GENETYX, Molecular Genetics Laboratory, Via Fermi 1, Marostica 36063, Vicenza, Italy
| | - Filippo Maria Ubaldi
- GENERA, Centers for Reproductive Medicine, Via G. De Notaris 2/B, Rome 00197, Italy.,GENETYX, Molecular Genetics Laboratory, Via Fermi 1, Marostica 36063, Vicenza, Italy
| | - Laura Rienzi
- GENERA, Centers for Reproductive Medicine, Via G. De Notaris 2/B, Rome 00197, Italy.,GENETYX, Molecular Genetics Laboratory, Via Fermi 1, Marostica 36063, Vicenza, Italy
| | - Richard Scott
- Reproductive Medicine Associates of New Jersey, 140 Allen Road, Basking Ridge, NJ 07920, USA
| | - Nathan Treff
- Reproductive Medicine Associates of New Jersey, 140 Allen Road, Basking Ridge, NJ 07920, USA
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16
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Keller A, Dziedzicka D, Zambelli F, Markouli C, Sermon K, Spits C, Geens M. Genetic and epigenetic factors which modulate differentiation propensity in human pluripotent stem cells. Hum Reprod Update 2018; 24:162-175. [PMID: 29377992 DOI: 10.1093/humupd/dmx042] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/23/2017] [Accepted: 12/22/2017] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Human pluripotent stem cell (hPSC) lines are known to have a bias in their differentiation. This gives individual cell lines a propensity to preferentially differentiate towards one germ layer or cell type over others. Chromosomal aberrations, mitochondrial mutations, genetic diversity and epigenetic variance are the main drivers of this phenomenon, and can lead to a wide range of phenotypes. OBJECTIVE AND RATIONALE Our aim is to provide a comprehensive overview of the different factors which influence differentiation propensity. Specifically, we sought to highlight known genetic variances and their mechanisms, in addition to more general observations from larger abnormalities. Furthermore, we wanted to provide an up-to-date list of a growing number of predictive indicators which are able to identify differentiation propensity before the initiation of differentiation. As differentiation propensity can lead to difficulties in both research as well as clinical translation, our thorough overview could be a useful tool. SEARCH METHODS Combinations of the following key words were applied as search criteria in the PubMed database: embryonic stem cells, induced pluripotent stem cells, differentiation propensity (also: potential, efficiency, capacity, bias, variability), epigenetics, chromosomal abnormalities, genetic aberrations, X chromosome inactivation, mitochondrial function, mitochondrial metabolism, genetic diversity, reprogramming, predictive marker, residual stem cell, clinic. Only studies in English were included, ranging from 2000 to 2017, with a majority ranging from 2010 to 1017. Further manuscripts were added from cross-references. OUTCOMES Differentiation propensity is affected by a wide variety of (epi)genetic factors. These factors clearly lead to a loss of differentiation capacity, preference towards certain cell types and oftentimes, phenotypes which begin to resemble cancer. Broad changes in (epi)genetics, such as aneuploidies or wide-ranging modifications to the epigenetic landscape tend to lead to extensive, less definite changes in differentiation capacity, whereas more specific abnormalities often have precise ramifications in which certain cell types become more preferential. Furthermore, there appears to be a greater, though often less considered, contribution to differentiation propensity by factors such as mitochondria and inherent genetic diversity. Varied differentiation capacity can also lead to potential consequences in the clinical translation of hPSC, including the occurrence of residual undifferentiated stem cells, and the transplantation of potentially transformed cells. WIDER IMPLICATIONS As hPSC continue to advance towards the clinic, our understanding of them progresses as well. As a result, the challenges faced become more numerous, but also more clear. If the transition to the clinic is to be achieved with a minimum number of potential setbacks, thorough evaluation of the cells will be an absolute necessity. Altered differentiation propensity represents at least one such hurdle, for which researchers and eventually clinicians will need to find solutions. Already, steps are being taken to tackle the issue, though further research will be required to evaluate any long-term risks it poses.
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Affiliation(s)
- Alexander Keller
- Research group Reproduction and Genetics (REGE), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Jette, Belgium
| | - Dominika Dziedzicka
- Research group Reproduction and Genetics (REGE), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Jette, Belgium
| | - Filippo Zambelli
- Research group Reproduction and Genetics (REGE), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Jette, Belgium
| | - Christina Markouli
- Research group Reproduction and Genetics (REGE), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Jette, Belgium
| | - Karen Sermon
- Research group Reproduction and Genetics (REGE), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Jette, Belgium
| | - Claudia Spits
- Research group Reproduction and Genetics (REGE), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Jette, Belgium
| | - Mieke Geens
- Research group Reproduction and Genetics (REGE), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Jette, Belgium
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Dziedzicka D, Markouli C, Barbé L, Spits C, Sermon K, Geens M. A High Proliferation Rate is Critical for Reproducible and Standardized Embryoid Body Formation from Laminin-521-Based Human Pluripotent Stem Cell Cultures. Stem Cell Rev Rep 2017; 12:721-730. [PMID: 27544201 DOI: 10.1007/s12015-016-9679-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
When aiming for homogenous embryoid body (EB) differentiation, the use of equal-sized EBs is required to avoid a size-induced differentiation bias. In this study we developed an efficient and standardized EB formation protocol for human pluripotent stem cells (hPSC) cultured in a laminin-521-based xeno-free system. As the cell proliferation rate of the cells growing on laminin-521 strongly affected the efficiency of aggregate formation, we found that recently passaged cells, as well as the addition of ROCK inhibitor, were essential for reproducible EB formation from hPSC single-cell suspensions. EBs could be obtained in a variety of differentiation media, in 96-well round-bottom plates and in hanging drops. Gene expression studies on differentially sized EBs from three individual human embryonic stem cell lines demonstrated that the medium used for differentiation influenced the differentiation outcome to a much greater extent than the number of cells used for the initial EB formation. Our findings give a new insight into factors that influence the EB formation and differentiation process. This optimized method allows us to easily manipulate EB formation and provide an excellent starting point for downstream EB-based differentiation protocols.
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Affiliation(s)
- Dominika Dziedzicka
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium.
| | - Christina Markouli
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium
| | - Lise Barbé
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium
| | - Claudia Spits
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium
| | - Karen Sermon
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium
| | - Mieke Geens
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium
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18
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Martin U. Genome stability of programmed stem cell products. Adv Drug Deliv Rev 2017; 120:108-117. [PMID: 28917518 DOI: 10.1016/j.addr.2017.09.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 08/31/2017] [Accepted: 09/07/2017] [Indexed: 01/23/2023]
Abstract
Inherited and acquired genomic abnormalities are known to cause genetic diseases and contribute to cancer formation. Recent studies demonstrated a substantial mutational load in mouse and human embryonic and induced pluripotent stem cells (ESCs and iPSCs). Single nucleotide variants, copy number variations, and larger chromosomal abnormalities may influence the differentiation capacity of pluripotent stem cells and the functionality of their derivatives in disease modeling and drug screening, and are considered a serious risk for cellular therapies based on ESC or iPSC derivatives. This review discusses the types and origins of different genetic abnormalities in pluripotent stem cells, methods for their detection, and the mechanisms of development and enrichment during reprogramming and culture expansion.
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Affiliation(s)
- Ulrich Martin
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH Cluster of Excellence, German Center for Lung Research, Hannover Medical School, Germany.
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DNA isolation protocol effects on nuclear DNA analysis by microarrays, droplet digital PCR, and whole genome sequencing, and on mitochondrial DNA copy number estimation. PLoS One 2017; 12:e0180467. [PMID: 28683077 PMCID: PMC5500342 DOI: 10.1371/journal.pone.0180467] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 06/15/2017] [Indexed: 01/08/2023] Open
Abstract
Potential bias introduced during DNA isolation is inadequately explored, although it could have significant impact on downstream analysis. To investigate this in human brain, we isolated DNA from cerebellum and frontal cortex using spin columns under different conditions, and salting-out. We first analysed DNA using array CGH, which revealed a striking wave pattern suggesting primarily GC-rich cerebellar losses, even against matched frontal cortex DNA, with a similar pattern on a SNP array. The aCGH changes varied with the isolation protocol. Droplet digital PCR of two genes also showed protocol-dependent losses. Whole genome sequencing showed GC-dependent variation in coverage with spin column isolation from cerebellum. We also extracted and sequenced DNA from substantia nigra using salting-out and phenol / chloroform. The mtDNA copy number, assessed by reads mapping to the mitochondrial genome, was higher in substantia nigra when using phenol / chloroform. We thus provide evidence for significant method-dependent bias in DNA isolation from human brain, as reported in rat tissues. This may contribute to array "waves", and could affect copy number determination, particularly if mosaicism is being sought, and sequencing coverage. Variations in isolation protocol may also affect apparent mtDNA abundance.
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20
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Barbé L, Lanni S, López-Castel A, Franck S, Spits C, Keymolen K, Seneca S, Tomé S, Miron I, Letourneau J, Liang M, Choufani S, Weksberg R, Wilson MD, Sedlacek Z, Gagnon C, Musova Z, Chitayat D, Shannon P, Mathieu J, Sermon K, Pearson CE. CpG Methylation, a Parent-of-Origin Effect for Maternal-Biased Transmission of Congenital Myotonic Dystrophy. Am J Hum Genet 2017; 100:488-505. [PMID: 28257691 PMCID: PMC5339342 DOI: 10.1016/j.ajhg.2017.01.033] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 01/26/2017] [Indexed: 12/13/2022] Open
Abstract
CTG repeat expansions in DMPK cause myotonic dystrophy (DM1) with a continuum of severity and ages of onset. Congenital DM1 (CDM1), the most severe form, presents distinct clinical features, large expansions, and almost exclusive maternal transmission. The correlation between CDM1 and expansion size is not absolute, suggesting contributions of other factors. We determined CpG methylation flanking the CTG repeat in 79 blood samples from 20 CDM1-affected individuals; 21, 27, and 11 individuals with DM1 but not CDM1 (henceforth non-CDM1) with maternal, paternal, and unknown inheritance; and collections of maternally and paternally derived chorionic villus samples (7 CVSs) and human embryonic stem cells (4 hESCs). All but two CDM1-affected individuals showed high levels of methylation upstream and downstream of the repeat, greater than non-CDM1 individuals (p = 7.04958 × 10−12). Most non-CDM1 individuals were devoid of methylation, where one in six showed downstream methylation. Only two non-CDM1 individuals showed upstream methylation, and these were maternally derived childhood onset, suggesting a continuum of methylation with age of onset. Only maternally derived hESCs and CVSs showed upstream methylation. In contrast, paternally derived samples (27 blood samples, 3 CVSs, and 2 hESCs) never showed upstream methylation. CTG tract length did not strictly correlate with CDM1 or methylation. Thus, methylation patterns flanking the CTG repeat are stronger indicators of CDM1 than repeat size. Spermatogonia with upstream methylation may not survive due to methylation-induced reduced expression of the adjacent SIX5, thereby protecting DM1-affected fathers from having CDM1-affected children. Thus, DMPK methylation may account for the maternal bias for CDM1 transmission, larger maternal CTG expansions, age of onset, and clinical continuum, and may serve as a diagnostic indicator.
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Jacobs K, Van de Velde H, De Paepe C, Sermon K, Spits C. Mitotic spindle disruption in human preimplantation embryos activates the spindle assembly checkpoint but not apoptosis until Day 5 of development. Mol Hum Reprod 2017; 23:321-329. [DOI: 10.1093/molehr/gax007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 01/31/2017] [Indexed: 12/22/2022] Open
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Lombard-Banek C, Moody SA, Nemes P. High-Sensitivity Mass Spectrometry for Probing Gene Translation in Single Embryonic Cells in the Early Frog ( Xenopus) Embryo. Front Cell Dev Biol 2016; 4:100. [PMID: 27761436 PMCID: PMC5050209 DOI: 10.3389/fcell.2016.00100] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/29/2016] [Indexed: 01/01/2023] Open
Abstract
Direct measurement of protein expression with single-cell resolution promises to deepen the understanding of the basic molecular processes during normal and impaired development. High-resolution mass spectrometry provides detailed coverage of the proteomic composition of large numbers of cells. Here we discuss recent mass spectrometry developments based on single-cell capillary electrophoresis that extend discovery proteomics to sufficient sensitivity to enable the measurement of proteins in single cells. The single-cell mass spectrometry system is used to detect a large number of proteins in single embryonic cells in the 16-cell embryo of the South African clawed frog (Xenopus laevis) that give rise to distinct tissue types. Single-cell measurements of protein expression provide complementary information on gene transcription during early development of the vertebrate embryo, raising a potential to understand how differential gene expression coordinates normal cell heterogeneity during development.
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Affiliation(s)
| | - Sally A Moody
- Department of Anatomy and Regenerative Biology, The George Washington University Washington, DC, USA
| | - Peter Nemes
- Department of Chemistry, The George Washington University Washington, DC, USA
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Sermon K, Capalbo A, Cohen J, Coonen E, De Rycke M, De Vos A, Delhanty J, Fiorentino F, Gleicher N, Griesinger G, Grifo J, Handyside A, Harper J, Kokkali G, Mastenbroek S, Meldrum D, Meseguer M, Montag M, Munné S, Rienzi L, Rubio C, Scott K, Scott R, Simon C, Swain J, Treff N, Ubaldi F, Vassena R, Vermeesch JR, Verpoest W, Wells D, Geraedts J. The why, the how and the when of PGS 2.0: current practices and expert opinions of fertility specialists, molecular biologists, and embryologists. Mol Hum Reprod 2016; 22:845-57. [PMID: 27256483 DOI: 10.1093/molehr/gaw034] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 05/16/2016] [Indexed: 01/11/2023] Open
Abstract
STUDY QUESTION We wanted to probe the opinions and current practices on preimplantation genetic screening (PGS), and more specifically on PGS in its newest form: PGS 2.0? STUDY FINDING Consensus is lacking on which patient groups, if any at all, can benefit from PGS 2.0 and, a fortiori, whether all IVF patients should be offered PGS. WHAT IS KNOWN ALREADY It is clear from all experts that PGS 2.0 can be defined as biopsy at the blastocyst stage followed by comprehensive chromosome screening and possibly combined with vitrification. Most agree that mosaicism is less of an issue at the blastocyst stage than at the cleavage stage but whether mosaicism is no issue at all at the blastocyst stage is currently called into question. STUDY DESIGN, SAMPLES/MATERIALS, METHODS A questionnaire was developed on the three major aspects of PGS 2.0: the Why, with general questions such as PGS 2.0 indications; the How, specifically on genetic analysis methods; the When, on the ideal method and timing of embryo biopsy. Thirty-five colleagues have been selected to address these questions on the basis of their experience with PGS, and demonstrated by peer-reviewed publications, presentations at meetings and participation in the discussion. The first group of experts who were asked about 'The Why' comprised fertility experts, the second group of molecular biologists were asked about 'The How' and the third group of embryologists were asked about 'The When'. Furthermore, the geographical distribution of the experts has been taken into account. Thirty have filled in the questionnaire as well as actively participated in the redaction of the current paper. MAIN RESULTS AND THE ROLE OF CHANCE The 30 participants were from Europe (Belgium, Germany, Greece, Italy, Netherlands, Spain, UK) and the USA. Array comparative genome hybridization is the most widely used method amongst the participants, but it is slowly being replaced by massive parallel sequencing. Most participants offering PGS 2.0 to their patients prefer blastocyst biopsy. The high efficiency of vitrification of blastocysts has added a layer of complexity to the discussion, and it is not clear whether PGS in combination with vitrification, PGS alone, or vitrification alone, followed by serial thawing and eSET will be the favoured approach. The opinions range from in favour of the introduction of PGS 2.0 for all IVF patients, over the proposal to use PGS as a tool to rank embryos according to their implantation potential, to scepticism towards PGS pending a positive outcome of robust, reliable and large-scale RCTs in distinct patient groups. LIMITATIONS, REASONS FOR CAUTION Care was taken to obtain a wide spectrum of views from carefully chosen experts. However, not all invited experts agreed to participate, which explains a lack of geographical coverage in some areas, for example China. This paper is a collation of current practices and opinions, and it was outside the scope of this study to bring a scientific, once-and-for-all solution to the ongoing debate. WIDER IMPLICATIONS OF THE FINDINGS This paper is unique in that it brings together opinions on PGS 2.0 from all different perspectives and gives an overview of currently applied technologies as well as potential future developments. It will be a useful reference for fertility specialists with an expertise outside reproductive genetics. LARGE SCALE DATA none. STUDY FUNDING AND COMPETING INTERESTS No specific funding was obtained to conduct this questionnaire.
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Affiliation(s)
- Karen Sermon
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Antonio Capalbo
- GENETYX, Molecular Genetics Laboratory, Via Fermi 1, 36063 Marostica (VI), Italy
| | - Jacques Cohen
- ART Institute of Washington at Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Edith Coonen
- Department of Reproductive Medicine, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX Maastricht, The Netherlands Department of Clinical Genetics, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX Maastricht, The Netherlands
| | - Martine De Rycke
- Centre for Medical Genetics, UZ Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Anick De Vos
- Centre for Reproductive Medicine, UZ Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Joy Delhanty
- University College London Centre for PGD, UCL, 86-96 Chenies Mews, London WC1E 6HX, UK
| | - Francesco Fiorentino
- GENOMA-Molecular Genetics Laboratories, Via di Castel Giubileo, 11 00138, Rome, Italy
| | - Norbert Gleicher
- The Center for Human Reproduction, New York, NY 10021, USA The Foundation for Reproductive Medicine, New York, NY 1022, USA The Rockefeller University, New York, NY 10065, USA
| | - Georg Griesinger
- Department of Reproductive Medicine and Gynecological Endocrinology, University Hospital of Schleswig-Holstein, Campus Luebeck, Ratzeburger Allee 160, 23538 Luebeck, Germany
| | - Jamie Grifo
- NYU Fertility Center, NYU Langone Medical Center, 660 1st Ave, New York, NY 10016, USA
| | - Alan Handyside
- The Bridge Centre, London SE1 9RY, UK Illumina Cambridge Ltd, Capital Park CPC4, Fulbourn, Cambridge CB21 5XE, UK
| | - Joyce Harper
- University College London Centre for PGD, UCL, 86-96 Chenies Mews, London WC1E 6HX, UK
| | - Georgia Kokkali
- Centre for Human Reproduction, Reproductive Medicine Unit, Genesis Athens Clinic, Papanicoli 14-16, Chalandri, 152-32, Athens, Greece
| | - Sebastiaan Mastenbroek
- Center for Reproductive Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - David Meldrum
- Division of Reproductive Endocrinology and Infertility, University of California San Diego, San Diego, CA, USA
| | - Marcos Meseguer
- Instituto Valenciano de Infertilidad (IVI) Clinic Valencia, Valencia, Spain
| | - Markus Montag
- ilabcomm GmbH, Eisenachstr. 34, 53757 Sankt Augustin, Germany
| | | | - Laura Rienzi
- GENERA, Centres for Reproductive Medicine, Rome, Italy
| | - Carmen Rubio
- Igenomix, and IVI Fundation, Parc Cientific Universitat de Valencia, Catedrático Agustín Escardino 9, 46980 Paterna, Valencia, Spain
| | | | - Richard Scott
- Reproductive Medicine Associates (RMA) of New Jersey, 140 Allen Road, Basking Ridge, NJ 07920, USA
| | - Carlos Simon
- Fundación Instituto Valenciano de Infertilidad, Department of Obstetrics and Gynecology, University of Valencia, Valencia, Spain INCLIVA Health Research Institute, Valencia, Spain IGenomix, Valencia, Spain
| | - Jason Swain
- CCRM IVF Laboratory Network, Englewood, CO 80112 USA
| | - Nathan Treff
- Reproductive Medicine Associates (RMA) of New Jersey, 140 Allen Road, Basking Ridge, NJ 07920, USA
| | | | - Rita Vassena
- Clinica EUGIN, Travessera de Les Corts 322, 08029 Barcelona, Spain
| | | | - Willem Verpoest
- Centre for Reproductive Medicine, UZ Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Dagan Wells
- Nuffield Department of Obstetrics and Gynaecology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK Reprogenetics UK, Institute of Reproductive Sciences, Oxford Business Park, Oxford OX4 2HW, UK
| | - Joep Geraedts
- Department of Reproductive Medicine, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX Maastricht, The Netherlands Department of Clinical Genetics, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX Maastricht, The Netherlands
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Techniques of Human Embryonic Stem Cell and Induced Pluripotent Stem Cell Derivation. Arch Immunol Ther Exp (Warsz) 2016; 64:349-70. [PMID: 26939778 PMCID: PMC5021740 DOI: 10.1007/s00005-016-0385-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 11/17/2015] [Indexed: 12/22/2022]
Abstract
Developing procedures for the derivation of human pluripotent stem cells (PSCs) gave rise to novel pathways into regenerative medicine research. For many years, stem cells have attracted attention as a potentially unlimited cell source for cellular therapy in neurodegenerative disorders, cardiovascular diseases, and spinal cord injuries, for example. In these studies, adult stem cells were insufficient; therefore, many attempts were made to obtain PSCs by other means. This review discusses key issues concerning the techniques of pluripotent cell acquisition. Technical and ethical issues hindered the medical use of somatic cell nuclear transfer and embryonic stem cells. Therefore, induced PSCs (iPSCs) emerged as a powerful technique with great potential for clinical applications, patient-specific disease modelling and pharmaceutical studies. The replacement of viral vectors or the administration of analogous proteins or chemical compounds during cell reprogramming are modifications designed to reduce tumorigenesis risk and to augment the procedure efficiency. Intensified analysis of new PSC lines revealed other barriers to overcome, such as epigenetic memory, disparity between human and mouse pluripotency, and variable response to differentiation of some iPSC lines. Thus, multidimensional verification must be conducted to fulfil strict clinical-grade requirements. Nevertheless, the first clinical trials in patients with spinal cord injury and macular dystrophy were recently carried out with differentiated iPSCs, encouraging alternative strategies for potential autologous cellular therapies.
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Jacobs K, Zambelli F, Mertzanidou A, Smolders I, Geens M, Nguyen HT, Barbé L, Sermon K, Spits C. Higher-Density Culture in Human Embryonic Stem Cells Results in DNA Damage and Genome Instability. Stem Cell Reports 2016; 6:330-41. [PMID: 26923824 PMCID: PMC4788786 DOI: 10.1016/j.stemcr.2016.01.015] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 01/24/2016] [Accepted: 01/25/2016] [Indexed: 12/01/2022] Open
Abstract
Human embryonic stem cells (hESC) show great promise for clinical and research applications, but their well-known proneness to genomic instability hampers the development to their full potential. Here, we demonstrate that medium acidification linked to culture density is the main cause of DNA damage and genomic alterations in hESC grown on feeder layers, and this even in the short time span of a single passage. In line with this, we show that increasing the frequency of the medium refreshments minimizes the levels of DNA damage and genetic instability. Also, we show that cells cultured on laminin-521 do not present this increase in DNA damage when grown at high density, although the (long-term) impact on their genomic stability remains to be elucidated. Our results explain the high levels of genome instability observed over the years by many laboratories worldwide, and show that the development of optimal culture conditions is key to solving this problem. Increased culture density induces DNA damage and genomic alterations in hESC Medium acidification due to lactic acid accumulation is the main driver More frequent medium refreshments rescues genomic integrity in high-density culture Laminin-521 reduces DNA damage but has no clear effect on genomic instability
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Affiliation(s)
- Kurt Jacobs
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium; Institute of Molecular Cancer Research, University of Zurich (UZH), Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Filippo Zambelli
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Afroditi Mertzanidou
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Ilse Smolders
- Research Group Experimental Neuropharmacology, Center for Neurosciences C4N, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Mieke Geens
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Ha Thi Nguyen
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium; Center for Molecular Biology, Institute of Research and Development, Duy Tan University, K7/25 Quang Trung, Danang 550000, Vietnam
| | - Lise Barbé
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Karen Sermon
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Claudia Spits
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium.
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Unrevealed mosaicism in the next-generation sequencing era. Mol Genet Genomics 2015; 291:513-30. [PMID: 26481646 PMCID: PMC4819561 DOI: 10.1007/s00438-015-1130-7] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 10/07/2015] [Indexed: 12/19/2022]
Abstract
Mosaicism refers to the presence in an individual of normal and abnormal cells that are genotypically distinct and are derived from a single zygote. The incidence of mosaicism events in the human body is underestimated as the genotypes in the mosaic ratio, especially in the low-grade mosaicism, stay unrevealed. This review summarizes various research outcomes and diagnostic questions in relation to different types of mosaicism. The impact of both tested biological material and applied method on the mosaicism detection rate is especially highlighted. As next-generation sequencing technologies constitute a promising methodological solution in mosaicism detection in the coming years, revisions in current diagnostic protocols are necessary to increase the detection rate of the unrevealed mosaicism events. Since mosaicism identification is a complex process, numerous examples of multistep mosaicism investigations are presented and discussed.
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27
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Spits C, Guzman L, Mertzanidou A, Jacobs K, Ortega-Hrepich C, Gilchrist RB, Thompson JG, De Vos M, Smitz J, Sermon K. Chromosome constitution of human embryos generated after in vitro maturation including 3-isobutyl-1-methylxanthine in the oocyte collection medium. Hum Reprod 2014; 30:653-63. [PMID: 25475586 DOI: 10.1093/humrep/deu329] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
STUDY QUESTION Do cleavage-stage embryos obtained from oocytes matured in vitro after pre-incubation with a phosphodiesterase inhibitor (IBMX) carry more chromosomal abnormalities than those generated from oocytes matured in vivo? SUMMARY ANSWER The rate and type of chromosomal abnormalities in normally developing cleavage-stage embryos generated with an in vitro maturation (IVM) system including pre-incubation with IBMX are not different from those observed in supernumerary embryos obtained from oocytes matured in vivo. WHAT IS KNOWN ALREADY Very limited information is available about the chromosomal constitution of IVM embryos. Previous studies were carried out using FISH on single biopsied blastomeres or arrested whole embryos and only provided fragmentary information on chromosomal abnormalities in IVM embryos. There is no systematic study of chromosomal abnormalities in all blastomeres of human Day 3 embryos with good morphology. STUDY DESIGN, SIZE, DURATION Between July 2012 and December 2012, 16 young (age <35 years old) egg donors underwent 18 IVM cycles for the generation of research embryos. Eighteen embryos developed to Day 3 and were analysed using array comparative genomic hybridization (aCGH). PARTICIPANTS/MATERIALS, SETTING, METHODS Immature oocytes were retrieved from 2 to 10 mm follicles after mild ovarian stimulation with gonadotrophins but without hCG ovulation trigger. At collection, oocytes were pre-incubated with 3-isobutyl-1-methylxanthine (IBMX), a phosphodiesterase inhibitor and matured in vitro. After IVM culture, mature oocytes were microinjected with sperm from a single donor. Embryos were cultured to Day 3 after ICSI and all blastomeres of 18 good-morphology embryos were collected individually for aCGH. MAIN RESULTS AND THE ROLE OF CHANCE Oocyte maturation rate in vitro was 50.2% (120/239). The mean fertilization rate was 68.3% (82/120) and 30.5% (25/82) of fertilized oocytes developed into a morphologically good quality embryo on Day 3 after ICSI. Of these, 18 embryos that developed well up to Day 3 were analysed using aCGH. Eighty of the 123 blastomeres analysed showed at least one chromosomal abnormality. Three out of eighteen embryos had completely normal cells. A single embryo carried a meiotic abnormality, 11 embryos were mosaic and three were chaotic. Although the aneuploidy data of this study are too limited to allow statistical analysis, these data are comparable to our own published data on the chromosome constitution of whole day 3 and day 4 embryos after conventional ART. LIMITATIONS, REASONS FOR CAUTION Array CGH technology determines relative quantification of chromosomal domains but does not allow for the visualization of chromosomal rearrangements, assessment of ploidy or detection of uniparental isodisomy. Conclusions drawn on segmental abnormalities should be treated with caution. Although the limited number of embryos analysed here precludes firm conclusions, they provide valuable data on possible causes of the reduced potential of IVM embryos. WIDER IMPLICATIONS OF THE FINDINGS This is the first study to describe the complete chromosome complement of all single blastomeres of good-morphology day 3 embryos obtained with IVM (including the presence of IBMX in a pre-incubation medium). The results demonstrate that a high proportion of good-morphology embryos are aneuploid and that there is no obvious increase in aneuploidies as a result of IVM which seems to suggest that the reduced efficiency of IVM technology compared with standard IVF may be accounted for by factors other than aneuploidy, such as cytoplasmic defects or reduced endometrial receptivity. STUDY FUNDING/COMPETING INTERESTS This study was funded by the TBM (Applied Biomedical Research with Societal Finality) programme of the IWT (Agency for Innovation through Science and Technology - Flanders, 110680) and by a Methusalem grant of the Vrije Universiteit Brussel. C.S. is a post-doctoral fellow of the Fund for Scientific Research Flanders (FWO - Vlaanderen). K.J. is a PhD student funded by the FWO. The University of Adelaide owns a patent family associated with IVM technologies that is licensed to Cook Medical. R.B.G. and J.G.T. are inventors. The remaining authors have no conflict of interest to declare.
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Affiliation(s)
- C Spits
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, 1090 Brussels, Belgium Centre for Reproductive Medicine, UZ Brussel, 1090 Brussels, Belgium
| | - L Guzman
- Research Group Follicle Biology, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - A Mertzanidou
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, 1090 Brussels, Belgium Centre for Reproductive Medicine, UZ Brussel, 1090 Brussels, Belgium
| | - K Jacobs
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, 1090 Brussels, Belgium Centre for Reproductive Medicine, UZ Brussel, 1090 Brussels, Belgium
| | - C Ortega-Hrepich
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, 1090 Brussels, Belgium Centre for Reproductive Medicine, UZ Brussel, 1090 Brussels, Belgium
| | - R B Gilchrist
- Discipline of Obstetrics & Gynaecology, School of Women's & Children's Health, University of New South Wales, Sydney, Australia
| | - J G Thompson
- Robinson Research Institute, School of Paediatrics and Reproductive Health, ARC Centre of Excellence for Nanoscale BioPhotonics, The University of Adelaide, Adelaide, Australia
| | - M De Vos
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, 1090 Brussels, Belgium Centre for Reproductive Medicine, UZ Brussel, 1090 Brussels, Belgium Research Group Follicle Biology, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - J Smitz
- Research Group Follicle Biology, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - K Sermon
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, 1090 Brussels, Belgium Centre for Reproductive Medicine, UZ Brussel, 1090 Brussels, Belgium
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Hovatta O, Rodin S, Antonsson L, Tryggvason K. Concise review: animal substance-free human embryonic stem cells aiming at clinical applications. Stem Cells Transl Med 2014; 3:1269-74. [PMID: 25298372 DOI: 10.5966/sctm.2014-0129] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Human embryonic stem cells have been considered the gold standard as a cell source for regenerative medicine since they were first cultured in 1998. They are pluripotent and can form principally all the cells types in the body. They are obtained from supernumerary human in vitro fertilization embryos that cannot be used for infertility treatment. Following studies on factors regulating pluripotency and differentiation, we now have techniques to establish and effectively expand these cells in animal substance-free conditions, even from single cells biopsied from eight-cell stage embryos in chemically defined feeder-free cultures. The genetic stability and absence of tumorigenic mutations can be determined. There are satisfactory animal tests for functionality and safety. The first clinical trials are ongoing for two indications: age-related macular degeneration and spinal cord injury.
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Affiliation(s)
- Outi Hovatta
- Departments of Clinical Science, Intervention and Technology and Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden; Cardiovascular and Metabolic Disorders Program, Duke-NUS Graduate Medical School, Singapore
| | - Sergey Rodin
- Departments of Clinical Science, Intervention and Technology and Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden; Cardiovascular and Metabolic Disorders Program, Duke-NUS Graduate Medical School, Singapore
| | - Liselotte Antonsson
- Departments of Clinical Science, Intervention and Technology and Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden; Cardiovascular and Metabolic Disorders Program, Duke-NUS Graduate Medical School, Singapore
| | - Karl Tryggvason
- Departments of Clinical Science, Intervention and Technology and Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden; Cardiovascular and Metabolic Disorders Program, Duke-NUS Graduate Medical School, Singapore
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29
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Nguyen HT, Markouli C, Geens M, Barbe L, Sermon K, Spits C. Human embryonic stem cells show low-grade microsatellite instability. Mol Hum Reprod 2014; 20:981-9. [DOI: 10.1093/molehr/gau059] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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