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Vitillo L, Anjum F, Hewitt Z, Laing O, Ababneh NA, Baker D, Barbaric I, Coffey PJ. Gain of 20q11.21 in human pluripotent stem cells enhances differentiation to retinal pigment epithelium. Stem Cell Res Ther 2025; 16:82. [PMID: 39985055 PMCID: PMC11846190 DOI: 10.1186/s13287-025-04196-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 01/29/2025] [Indexed: 02/24/2025] Open
Abstract
BACKGROUND Cell therapies based on human pluripotent stem cells (hPSCs) are in clinical trials with the aim of restoring vision in people with age-related macular degeneration. The final cell therapy product consists of retinal pigment epithelium (RPE) cells differentiated from hPSCs. However, hPSCs recurrently acquire genetic abnormalities that give them an advantage in culture with unknown effects to the clinically-relevant cell progeny. One of the most common genetic abnormalities in hPSCs is the sub-karyotype 20q11.21 copy number variant, known to carry oncogenes. Understanding the impact of this variant on RPE differentiation and its potential for malignant transformation is crucial for the development of safe and effective cell therapies. METHODS We monitored the RPE differentiation efficiency of hPSCs with or without the 20q11.21 variant. We then phenotyped the purified RPE cells for functionality, purity and tumorigenicity potential. RESULTS We observed that 20q11.21 clones exhibited an enhanced differentiation capacity, developing pigmented foci at a higher rate and yield compared to normal clones. Gene expression analysis confirmed the upregulation of key RPE markers in 20q11.21 clones. The enhanced differentiation capacity of 20q11.21 clones was found to be dependent on the activity of BCL-XL, located within the amplicon. Furthermore, we demonstrated that 20q11.21-containing RPE cells displayed a mature phenotype, maintained long-term stability, and exhibited no malignant transformation capacity in vitro. CONCLUSION We demonstrated that gain of 20q11.21 enhances the speed and yield of RPE differentiation without compromising the phenotype of the derivatives. Finally, we discovered that 20q11.21-localised BCL-XL is important for RPE differentiation with potential non-canonical roles in retinal biology.
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Affiliation(s)
- Loriana Vitillo
- Rescue, Repair and Regeneration, Institute of Ophthalmology, University College London, London, EC1V 9EL, UK.
| | - Fabiha Anjum
- Rescue, Repair and Regeneration, Institute of Ophthalmology, University College London, London, EC1V 9EL, UK
| | - Zoe Hewitt
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, S10 2TN, UK
| | - Owen Laing
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, S10 2TN, UK
| | - Nidaa A Ababneh
- Cell Therapy Center, The University of Jordan, Amman, Jordan
| | - Duncan Baker
- Sheffield Diagnostic Genetic Services, Sheffield Children's Hospital, Sheffield, S10 2TH, UK
| | - Ivana Barbaric
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, S10 2TN, UK
| | - Peter J Coffey
- Rescue, Repair and Regeneration, Institute of Ophthalmology, University College London, London, EC1V 9EL, UK
- Centre for Stem Cell Biology and Engineering, University of California Santa Barbara, Santa Barbara, CA, USA
- NIHR Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust, UCL Institute of Ophthalmology, London, UK
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Lei Y, Duong MC, Krivec N, Janssens C, Regin M, Huyghebaert A, Couvreu de Deckersberg E, Sermon K, Al Delbany D, Spits C. Loss of 18q Alters TGFβ Signalling Affecting Anteroposterior Neuroectodermal Fate in Human Embryonic Stem Cells. Cell Prolif 2025:e13813. [PMID: 39908990 DOI: 10.1111/cpr.13813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2024] [Revised: 01/06/2025] [Accepted: 01/11/2025] [Indexed: 02/07/2025] Open
Abstract
Chromosomal abnormalities acquired during cell culture can compromise the differentiation potential of human pluripotent stem cells (hPSCs). In this work, we identified a diminished differentiation capacity to retinal progenitor cells in human embryonic stem cells (hESCs) with complex karyotypes that had in common the loss of part of chromosome 18q. Time-course gene-expression analysis during spontaneous differentiation and single-cell RNA sequencing found that these variant cell lines poorly specified into anterior neuroectoderm, and, when progressing through differentiation, they yielded poorly pigmented cells, with proliferating and pluripotent cell populations. The variant cell lines showed dysregulation of TGFβ signalling during differentiation, and chemical modulation of the TGFβ pathways showed that the basis of the improper specification was due to imbalances in the anteroposterior neuroectodermal fate commitment.
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Affiliation(s)
- Yingnan Lei
- Vrije Universiteit Brussel (VUB), Brussels Health Campus/Faculty of Medicine and Pharmacy, Research Group Genetics, Reproduction and Development, Brussels, Belgium
| | - Mai Chi Duong
- Vrije Universiteit Brussel (VUB), Brussels Health Campus/Faculty of Medicine and Pharmacy, Research Group Genetics, Reproduction and Development, Brussels, Belgium
- Department of Biochemistry, Ho Chi Minh city, Vietnam
| | - Nuša Krivec
- Vrije Universiteit Brussel (VUB), Brussels Health Campus/Faculty of Medicine and Pharmacy, Research Group Genetics, Reproduction and Development, Brussels, Belgium
| | - Charlotte Janssens
- Vrije Universiteit Brussel (VUB), Brussels Health Campus/Faculty of Medicine and Pharmacy, Research Group Genetics, Reproduction and Development, Brussels, Belgium
| | - Marius Regin
- Vrije Universiteit Brussel (VUB), Brussels Health Campus/Faculty of Medicine and Pharmacy, Research Group Genetics, Reproduction and Development, Brussels, Belgium
| | - Anfien Huyghebaert
- Vrije Universiteit Brussel (VUB), Brussels Health Campus/Faculty of Medicine and Pharmacy, Research Group Genetics, Reproduction and Development, Brussels, Belgium
| | - Edouard Couvreu de Deckersberg
- Vrije Universiteit Brussel (VUB), Brussels Health Campus/Faculty of Medicine and Pharmacy, Research Group Genetics, Reproduction and Development, Brussels, Belgium
| | - Karen Sermon
- Vrije Universiteit Brussel (VUB), Brussels Health Campus/Faculty of Medicine and Pharmacy, Research Group Genetics, Reproduction and Development, Brussels, Belgium
| | - Diana Al Delbany
- Vrije Universiteit Brussel (VUB), Brussels Health Campus/Faculty of Medicine and Pharmacy, Research Group Genetics, Reproduction and Development, Brussels, Belgium
| | - Claudia Spits
- Vrije Universiteit Brussel (VUB), Brussels Health Campus/Faculty of Medicine and Pharmacy, Research Group Genetics, Reproduction and Development, Brussels, Belgium
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Vales JP, Barbaric I. Culture-acquired genetic variation in human pluripotent stem cells: Twenty years on. Bioessays 2024; 46:e2400062. [PMID: 38873900 PMCID: PMC11589660 DOI: 10.1002/bies.202400062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 06/02/2024] [Accepted: 06/05/2024] [Indexed: 06/15/2024]
Abstract
Genetic changes arising in human pluripotent stem cells (hPSC) upon culture may bestow unwanted or detrimental phenotypes to cells, thus potentially impacting on the applications of hPSCs for clinical use and basic research. In the 20 years since the first report of culture-acquired genetic aberrations in hPSCs, a characteristic spectrum of recurrent aberrations has emerged. The preponderance of such aberrations implies that they provide a selective growth advantage to hPSCs upon expansion. However, understanding the consequences of culture-acquired variants for specific applications in cell therapy or research has been more elusive. The rapid progress of hPSC-based therapies to clinics is galvanizing the field to address this uncertainty and provide definitive ways both for risk assessment of variants and reducing their prevalence in culture. Here, we aim to provide a timely update on almost 20 years of research on this fascinating, but a still unresolved and concerning, phenomenon.
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Affiliation(s)
- John P. Vales
- Centre for Stem Cell BiologySchool of BiosciencesUniversity of SheffieldSheffieldUK
- Neuroscience InstituteUniversity of SheffieldSheffieldUK
- INSIGNEO InstituteUniversity of SheffieldSheffieldUK
| | - Ivana Barbaric
- Centre for Stem Cell BiologySchool of BiosciencesUniversity of SheffieldSheffieldUK
- Neuroscience InstituteUniversity of SheffieldSheffieldUK
- INSIGNEO InstituteUniversity of SheffieldSheffieldUK
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Krivec N, Couvreu de Deckersberg E, Lei Y, Al Delbany D, Regin M, Verhulst S, van Grunsven LA, Sermon K, Spits C. Gain of 1q confers an MDM4-driven growth advantage to undifferentiated and differentiating hESC while altering their differentiation capacity. Cell Death Dis 2024; 15:852. [PMID: 39572522 PMCID: PMC11582570 DOI: 10.1038/s41419-024-07236-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 11/05/2024] [Accepted: 11/08/2024] [Indexed: 11/24/2024]
Abstract
Gain of 1q is a highly recurrent chromosomal abnormality in human pluripotent stem cells. In this work, we show that gains of 1q impact the differentiation capacity to derivates of the three germ layers, leading to mis-specification to cranial placode and non-neural ectoderm during neuroectoderm differentiation. Also, we found a weaker expression of lineage-specific markers in hepatoblasts and cardiac progenitors. Competition assays show that the cells retain their selective advantage during differentiation, which is mediated by a higher expression of MDM4, a gene located in the common region of gain. MDM4 drives the winner phenotype of the mutant cells in both the undifferentiated and differentiating state by reducing the cells' sensitivity to DNA damage through decreased p53-mediated apoptosis. Finally, we found that cell density in culture plays a key role in promoting the competitive advantage of the cells by increasing DNA damage.
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Affiliation(s)
- Nuša Krivec
- Research Group Genetics, Reproduction and Development, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, 1090, Brussels, Belgium
| | - Edouard Couvreu de Deckersberg
- Research Group Genetics, Reproduction and Development, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, 1090, Brussels, Belgium
| | - Yingnan Lei
- Research Group Genetics, Reproduction and Development, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, 1090, Brussels, Belgium
| | - Diana Al Delbany
- Research Group Genetics, Reproduction and Development, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, 1090, Brussels, Belgium
| | - Marius Regin
- Research Group Genetics, Reproduction and Development, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, 1090, Brussels, Belgium
| | - Stefaan Verhulst
- Liver Cell Biology Research Group, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, 1090, Brussels, Belgium
| | - Leo A van Grunsven
- Liver Cell Biology Research Group, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, 1090, Brussels, Belgium
| | - Karen Sermon
- Research Group Genetics, Reproduction and Development, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, 1090, Brussels, Belgium
| | - Claudia Spits
- Research Group Genetics, Reproduction and Development, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, 1090, Brussels, Belgium.
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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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Andrysiak K, Stępniewski J, Spaczyńska-Boczar M, Łapicka-Bodzioch K, Słowik A, Dulak J. Generation of Human-Induced Pluripotent Stem Cells from Peripheral Blood Mononuclear Cells of C9ORF72-Associated Amyotrophic Lateral Sclerosis Patients. Methods Mol Biol 2024; 2835:135-146. [PMID: 39105912 DOI: 10.1007/978-1-0716-3995-5_12] [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] [Indexed: 08/07/2024]
Abstract
Disease modeling of neuromuscular disorders, such as amyotrophic lateral sclerosis (ALS), is hindered by limited accessibility of affected cells. This problem can be overcome by generation of human induced pluripotent stem cells (hiPSC), which can be then differentiated into required cells. Here, we describe the detailed protocol of hiPSC establishment from peripheral blood mononuclear cells (PBMC) of two ALS patients with detected expansion of G4C2 (GGGGCC) repeats in the first intron of C9ORF72 gene, known to be linked with the most common form of familial ALS.Successful PBMC reprogramming with non-integrating Sendai vectors was confirmed by expression of pluripotency markers: OCT4, NANOG, SSEA4, and TRA-1-60 in obtained hiPSC and their ability to differentiate into cells of three germ layers.The generated ALS-patient-specific hiPSC create a possibility for deciphering molecular basis of this devastating neuromuscular disease.
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Affiliation(s)
- Kalina Andrysiak
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, Kraków, Poland
| | - Jacek Stępniewski
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, Kraków, Poland.
| | | | | | - Agnieszka Słowik
- Department of Neurology, Jagiellonian University Medical College, Krakow, Poland
| | - Józef Dulak
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, Kraków, Poland.
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