1
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Furlanetto F, Flegel N, Kremp M, Spear C, Fröb F, Alfonsetti M, Bohl B, Krumbiegel M, Turan S, Reis A, Lie DC, Winkler J, Falk S, Wegner M, Karow M. A novel human organoid model system reveals requirement of TCF4 for oligodendroglial differentiation. Life Sci Alliance 2025; 8:e202403102. [PMID: 40155049 PMCID: PMC11953572 DOI: 10.26508/lsa.202403102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2024] [Revised: 03/19/2025] [Accepted: 03/19/2025] [Indexed: 04/01/2025] Open
Abstract
Heterozygous mutations of TCF4 in humans cause Pitt-Hopkins syndrome, a neurodevelopmental disease associated with intellectual disability and brain malformations. Although most studies focus on the role of TCF4 in neural stem cells and neurons, we here set out to assess the implication of TCF4 for oligodendroglial differentiation. We discovered that both monoallelic and biallelic mutations in TCF4 result in a diminished capacity to differentiate human neural progenitor cells toward myelinating oligodendrocytes through the forced expression of the transcription factors SOX10, OLIG2, and NKX6.2. Using this experimental strategy, we established a novel organoid model, which generates oligodendroglial cells within a human neurogenic tissue-like context. Also, here we found a reduced ability of TCF4 heterozygous cells to differentiate toward oligodendroglial cells. In sum, we establish a role of human TCF4 in oligodendrocyte differentiation and provide a model system, which allows to dissect the disease etiology in a human tissue-like context.
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Affiliation(s)
- Federica Furlanetto
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Nicole Flegel
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Marco Kremp
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Chiara Spear
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Franziska Fröb
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Margherita Alfonsetti
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Bettina Bohl
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Mandy Krumbiegel
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Sören Turan
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Andre Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Dieter C Lie
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Institute of Anatomy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jürgen Winkler
- Department of Molecular Neurology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Sven Falk
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Michael Wegner
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Marisa Karow
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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2
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Montilla‐Rojo J, Eleveld TF, van Soest M, Hillenius S, Timmerman DM, Gillis AJM, Roelen BAJ, Mummery CL, Looijenga LHJ, Salvatori DCF. Depletion of TP53 in Human Pluripotent Stem Cells Triggers Malignant-Like Behavior. Adv Biol (Weinh) 2025; 9:e2400538. [PMID: 39760438 PMCID: PMC12001006 DOI: 10.1002/adbi.202400538] [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: 09/12/2024] [Revised: 12/18/2024] [Indexed: 01/07/2025]
Abstract
Human pluripotent stem cells (hPSCs) tend to acquire genetic aberrations upon culture in vitro. Common aberrations are mutations in the tumor suppressor TP53, suspected to confer a growth-advantage to the mutant cells. However, their full impact in the development of malignant features and safety of hPSCs for downstream applications is yet to be elucidated. Here, TP53 is knocked out in hPSCs using CRISPR-Cas9 and compared them with isogenic wild-type hPSCs and human germ cell tumor lines as models of malignancy. While no major changes in proliferation, pluripotency, and transcriptomic profiles are found, mutant lines display aberrations in some of the main chromosomal hotspots for genetic abnormalities in hPSCs. Additionally, enhanced clonogenic and anchorage-free growth, alongside resistance to chemotherapeutic compounds is observed. The results indicate that common TP53-depleting mutations in hPSCs, although potentially overlooked by standard analyses, can impact their behavior and safety in a clinical setting.
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Affiliation(s)
- Joaquin Montilla‐Rojo
- Anatomy and PhysiologyDepartment Clinical SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrecht3584 CLThe Netherlands
| | - Thomas F. Eleveld
- Princess Máxima Center for Pediatric OncologyUtrecht3584 CSThe Netherlands
| | - Marnix van Soest
- Anatomy and PhysiologyDepartment Clinical SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrecht3584 CLThe Netherlands
| | - Sanne Hillenius
- Princess Máxima Center for Pediatric OncologyUtrecht3584 CSThe Netherlands
| | | | - Ad J. M. Gillis
- Princess Máxima Center for Pediatric OncologyUtrecht3584 CSThe Netherlands
| | - Bernard A. J. Roelen
- Anatomy and PhysiologyDepartment Clinical SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrecht3584 CLThe Netherlands
| | - Christine L. Mummery
- Department of Anatomy and EmbryologyLeiden University Medical CentreLeiden2333 ZCThe Netherlands
| | - Leendert H. J. Looijenga
- Princess Máxima Center for Pediatric OncologyUtrecht3584 CSThe Netherlands
- Department of PathologyUniversity Medical Center UtrechtUtrecht3584 CXThe Netherlands
| | - Daniela C. F. Salvatori
- Anatomy and PhysiologyDepartment Clinical SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrecht3584 CLThe Netherlands
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3
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Aygar S, Daheron L. Generation of a human iPSC line with Notch3 R133C mutation by CRISPR/Cas9: A tool for investigating CADASIL and therapeutic targets. Stem Cell Res 2025; 84:103678. [PMID: 39983483 DOI: 10.1016/j.scr.2025.103678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2025] [Accepted: 02/10/2025] [Indexed: 02/23/2025] Open
Abstract
Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a rare neuro vascular disease that is caused by mutations in Notch3. Here, we developed an iPSC line harboring the R133C mutation in Notch3, which is among the most common mutations leading to CADASIL. This mutation alters the disulfide bonding pattern leading to Notch3 protein aggregation, granular osmiophilic material (GOM) formation and vascular changes. The iPSC line was generated using CRISPR/Cas9 and edits were confirmed by PCR and Sanger sequencing. This resource is a valuable tool for studying molecular mechanisms of CADASIL and enabling the development and screening of targeted therapies for Notch3-related pathologies.
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Affiliation(s)
- Sema Aygar
- Harvard University Harvard Stem Cell Institute IPS Core Facility Cambridge USA
| | - Laurence Daheron
- Harvard University Harvard Stem Cell Institute IPS Core Facility Cambridge USA.
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4
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Nityanandam A, Patton MH, Bayazitov IT, Newman KD, Thomas KT, Zakharenko SS. Protocol for generating human assembloids to investigate thalamocortical and corticothalamic synaptic transmission and plasticity. STAR Protoc 2025; 6:103630. [PMID: 39921865 PMCID: PMC11850219 DOI: 10.1016/j.xpro.2025.103630] [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: 10/28/2024] [Revised: 12/05/2024] [Accepted: 01/15/2025] [Indexed: 02/10/2025] Open
Abstract
Human induced pluripotent stem cells (hiPSCs) can be used to generate assembloids that recreate thalamocortical circuitry displaying short-term and long-term synaptic plasticity. Here, we describe a protocol for differentiating hiPSCs into thalamic and cortical organoids and then fusing them to generate thalamocortical assembloids. We detail the steps for using whole-cell patch-clamp electrophysiology to investigate the properties of synaptic transmission and synaptic plasticity in this model system. For complete details on the use and execution of this protocol, please refer to Patton et al.1.
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Affiliation(s)
- Anjana Nityanandam
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Mary H Patton
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ildar T Bayazitov
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kyle D Newman
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kristen T Thomas
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Stanislav S Zakharenko
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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5
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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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6
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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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7
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Smith A. Propagating pluripotency - The conundrum of self-renewal. Bioessays 2024; 46:e2400108. [PMID: 39180242 PMCID: PMC11589686 DOI: 10.1002/bies.202400108] [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: 04/30/2024] [Revised: 07/29/2024] [Accepted: 08/06/2024] [Indexed: 08/26/2024]
Abstract
The discovery of mouse embryonic stem cells in 1981 transformed research in mammalian developmental biology and functional genomics. The subsequent generation of human pluripotent stem cells (PSCs) and the development of molecular reprogramming have opened unheralded avenues for drug discovery and cell replacement therapy. Here, I review the history of PSCs from the perspective that long-term self-renewal is a product of the in vitro signaling environment, rather than an intrinsic feature of embryos. I discuss the relationship between pluripotent states captured in vitro to stages of epiblast in the embryo and suggest key considerations for evaluation of PSCs. A remaining fundamental challenge is to determine whether naïve pluripotency can be propagated from the broad range of mammals by exploiting common principles in gene regulatory architecture.
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Affiliation(s)
- Austin Smith
- Living Systems InstituteUniversity of ExeterExeterUK
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8
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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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9
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Madrid M, Lakshmipathy U, Zhang X, Bharti K, Wall DM, Sato Y, Muschler G, Ting A, Smith N, Deguchi S, Kawamata S, Moore JC, Makovoz B, Sullivan S, Falco V, Al-Riyami AZ. Considerations for the development of iPSC-derived cell therapies: a review of key challenges by the JSRM-ISCT iPSC Committee. Cytotherapy 2024; 26:1382-1399. [PMID: 38958627 PMCID: PMC11471376 DOI: 10.1016/j.jcyt.2024.05.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 05/16/2024] [Accepted: 05/22/2024] [Indexed: 07/04/2024]
Abstract
Since their first production in 2007, human induced pluripotent stem cells (iPSCs) have provided a novel platform for the development of various cell therapies targeting a spectrum of diseases, ranging from rare genetic eye disorders to cancer treatment. However, several challenges must be tackled for iPSC-based cell therapy to enter the market and achieve broader global adoption. This white paper, authored by the Japanese Society for Regenerative Medicine (JSRM) - International Society for Cell Therapy (ISCT) iPSC Committee delves into the hurdles encountered in the pursuit of safe and economically viable iPSC-based therapies, particularly from the standpoint of the cell therapy industry. It discusses differences in global guidelines and regulatory frameworks, outlines a series of quality control tests required to ensure the safety of the cell therapy, and provides details and important considerations around cost of goods (COGs), including the impact of automated advanced manufacturing.
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Affiliation(s)
| | | | | | - Kapil Bharti
- National Eye Institute of the National Institutes of Health, Bethesda, USA
| | - Dominic M Wall
- Peter MacCallum Cancer Centre, Melbourne Australia; Cell Therapies Pty Ltd, Melbourne, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia
| | - Yoji Sato
- National Institute of Health Sciences, Kawasaki, Japan
| | | | | | | | - Shuhei Deguchi
- CIRA Foundation, Facility for iPS Cell Therapy (FiT), Kyoto, Japan
| | - Shin Kawamata
- Cyto-Facto Inc., Kobe, Japan; Kobe University, Kobe, Japan.
| | | | | | | | | | - Arwa Z Al-Riyami
- Department of Hematology, Sultan Qaboos University Hospital, University Medical City, Muscat, Oman
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10
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Kim YJ, Kang B, Kweon S, Oh S, Kim D, Gil D, Lee H, Kim JH, Ju JH, Roh TY, Hong CP, Cha HJ. Longitudinal analysis of genetic and epigenetic changes in human pluripotent stem cells in the landscape of culture-induced abnormality. Exp Mol Med 2024; 56:2409-2422. [PMID: 39482531 PMCID: PMC11612254 DOI: 10.1038/s12276-024-01334-8] [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: 04/06/2024] [Revised: 06/10/2024] [Accepted: 07/23/2024] [Indexed: 11/03/2024] Open
Abstract
Human embryonic stem cells (hESCs) are naturally equipped to maintain genome integrity to minimize genetic mutations during early embryo development. However, genetic aberration risks and subsequent cellular changes in hESCs during in vitro culture pose a significant threat to stem cell therapy. While a few studies have reported specific somatic mutations and copy number variations (CNVs), the molecular mechanisms underlying the acquisition of 'culture-adapted phenotypes' by hESCs are largely unknown. Therefore, we conducted comprehensive genomic, single-cell transcriptomic, and single-cell ATAC-seq analyses of an isogenic hESC model displaying definitive 'culture-adapted phenotypes'. We found that hESCs lacking TP53, in which loss-of-function mutations were identified in human pluripotent stem cells (hPSCs), presented a surge in somatic mutations. Notably, hPSCs with a copy number gain of 20q11.21 during early passage did not present 'culture-adapted phenotypes' or BCL2L1 induction. Single-cell RNA-seq and ATAC-seq analyses revealed active transcriptional regulation at the 20q11.21 locus. Furthermore, the induction of BCL2L1 and TPX2 to trigger 'culture-adapted phenotypes' was associated with epigenetic changes facilitating TEA domain (TEAD) binding. These results suggest that 20q11.21 copy number gain and additional epigenetic changes are necessary for expressing 'culture-adapted phenotypes' by activating gene transcription at this specific locus.
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Affiliation(s)
- Yun-Jeong Kim
- College of Pharmacy, Seoul National University, Seoul, Republic of Korea
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Byunghee Kang
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Solbi Kweon
- Theragen Bio, Co., Ltd., Seongnam, Republic of Korea
| | - Sejin Oh
- Theragen Bio, Co., Ltd., Seongnam, Republic of Korea
| | - Dayeon Kim
- College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Dayeon Gil
- Korea National Stem Cell Bank, Cheongju, Republic of Korea
- Division of Intractable Disease Research, Department of Chronic Disease Convergence Research, Korea National Institute of Health, Osong Health Technology Administration Complex, Cheongju, Republic of Korea
| | - Hyeonji Lee
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Jung-Hyun Kim
- Korea National Stem Cell Bank, Cheongju, Republic of Korea
- Division of Intractable Disease Research, Department of Chronic Disease Convergence Research, Korea National Institute of Health, Osong Health Technology Administration Complex, Cheongju, Republic of Korea
- College of Pharmacy, Ajou University, Suwon, Republic of Korea
| | - Ji Hyeon Ju
- YiPSCELL Inc., Seoul, Republic of Korea
- Catholic iPSC Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Division of Rheumatology, Department of Internal Medicine, Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul St. Mary's Hospital, Seoul, Republic of Korea
| | - Tae-Young Roh
- Department of Life Sciences, Ewha Womans University, Seoul, Republic of Korea.
| | | | - Hyuk-Jin Cha
- College of Pharmacy, Seoul National University, Seoul, Republic of Korea.
- Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea.
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11
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Massafret O, Barragán M, Álvarez-González L, Aran B, Martín-Mur B, Esteve-Codina A, Ruiz-Herrera A, Ibáñez E, Santaló J. The pluripotency state of human embryonic stem cells derived from single blastomeres of eight-cell embryos. Cells Dev 2024; 179:203935. [PMID: 38914137 DOI: 10.1016/j.cdev.2024.203935] [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: 04/26/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 06/26/2024]
Abstract
Human embryonic stem cells (hESCs) derived from blastocyst stage embryos present a primed state of pluripotency, whereas mouse ESCs (mESCs) display naïve pluripotency. Their unique characteristics make naïve hESCs more suitable for particular applications in biomedical research. This work aimed to derive hESCs from single blastomeres and determine their pluripotency state, which is currently unclear. We derived hESC lines from single blastomeres of 8-cell embryos and from whole blastocysts, and analysed several naïve pluripotency indicators, their transcriptomic profile and their trilineage differentiation potential. No significant differences were observed between blastomere-derived hESCs (bm-hESCs) and blastocyst-derived hESCs (bc-hESCs) for most naïve pluripotency indicators, including TFE3 localization, mitochondrial activity, and global DNA methylation and hydroxymethylation, nor for their trilineage differentiation potential. Nevertheless, bm-hESCs showed an increased single-cell clonogenicity and a higher expression of naïve pluripotency markers at early passages than bc-hESCs. Furthermore, RNA-seq revealed that bc-hESCs overexpressed a set of genes related to the post-implantational epiblast. Altogether, these results suggest that bm-hESCs, although displaying primed pluripotency, would be slightly closer to the naïve end of the pluripotency continuum than bc-hESCs.
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Affiliation(s)
- Ot Massafret
- Genome Integrity and Reproductive Biology Group, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Bioengineering in Reproductive Health, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Montserrat Barragán
- Basic Research Laboratory, Eugin Group, Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - Lucía Álvarez-González
- Genome Integrity and Reproductive Biology Group, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Begoña Aran
- Stem Cell Bank, Regenerative Medicine Program, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), 08908 L'Hospitalet de Llobregat, Spain
| | - Beatriz Martín-Mur
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Anna Esteve-Codina
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain.; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Aurora Ruiz-Herrera
- Genome Integrity and Reproductive Biology Group, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Elena Ibáñez
- Genome Integrity and Reproductive Biology Group, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| | - Josep Santaló
- Genome Integrity and Reproductive Biology Group, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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12
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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 PMCID: PMC11353044 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; (D.A.D.); (M.S.G.); (N.K.); (A.H.); (M.R.); (M.C.D.); (Y.L.); (K.S.); (C.O.)
| | - Manjusha S. Ghosh
- Research Group Genetics, Reproduction and Development, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium; (D.A.D.); (M.S.G.); (N.K.); (A.H.); (M.R.); (M.C.D.); (Y.L.); (K.S.); (C.O.)
| | - Nuša Krivec
- Research Group Genetics, Reproduction and Development, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium; (D.A.D.); (M.S.G.); (N.K.); (A.H.); (M.R.); (M.C.D.); (Y.L.); (K.S.); (C.O.)
| | - Anfien Huyghebaert
- Research Group Genetics, Reproduction and Development, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium; (D.A.D.); (M.S.G.); (N.K.); (A.H.); (M.R.); (M.C.D.); (Y.L.); (K.S.); (C.O.)
| | - Marius Regin
- Research Group Genetics, Reproduction and Development, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium; (D.A.D.); (M.S.G.); (N.K.); (A.H.); (M.R.); (M.C.D.); (Y.L.); (K.S.); (C.O.)
| | - Mai Chi Duong
- Research Group Genetics, Reproduction and Development, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium; (D.A.D.); (M.S.G.); (N.K.); (A.H.); (M.R.); (M.C.D.); (Y.L.); (K.S.); (C.O.)
- 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; (D.A.D.); (M.S.G.); (N.K.); (A.H.); (M.R.); (M.C.D.); (Y.L.); (K.S.); (C.O.)
| | - Karen Sermon
- Research Group Genetics, Reproduction and Development, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium; (D.A.D.); (M.S.G.); (N.K.); (A.H.); (M.R.); (M.C.D.); (Y.L.); (K.S.); (C.O.)
| | - Catharina Olsen
- Research Group Genetics, Reproduction and Development, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium; (D.A.D.); (M.S.G.); (N.K.); (A.H.); (M.R.); (M.C.D.); (Y.L.); (K.S.); (C.O.)
- 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; (D.A.D.); (M.S.G.); (N.K.); (A.H.); (M.R.); (M.C.D.); (Y.L.); (K.S.); (C.O.)
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13
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Stavish D, Price CJ, Gelezauskaite G, Alsehli H, Leonhard KA, Taapken SM, McIntire EM, Laing O, James BM, Riley JJ, Zerbib J, Baker D, Harding AL, Jestice LH, Eleveld TF, Gillis AJM, Hillenius S, Looijenga LHJ, Gokhale PJ, Ben-David U, Ludwig TE, Barbaric I. Feeder-free culture of human pluripotent stem cells drives MDM4-mediated gain of chromosome 1q. Stem Cell Reports 2024; 19:1217-1232. [PMID: 38964325 PMCID: PMC11368687 DOI: 10.1016/j.stemcr.2024.06.003] [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: 05/24/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 07/06/2024] Open
Abstract
Culture-acquired variants in human pluripotent stem cells (hPSCs) hinder their applications in research and clinic. However, the mechanisms that underpin selection of variants remain unclear. Here, through analysis of comprehensive karyotyping datasets from over 23,000 hPSC cultures of more than 1,500 lines, we explored how culture conditions shape variant selection. Strikingly, we identified an association of chromosome 1q gains with feeder-free cultures and noted a rise in its prevalence in recent years, coinciding with increased usage of feeder-free regimens. Competition experiments of multiple isogenic lines with and without a chromosome 1q gain confirmed that 1q variants have an advantage in feeder-free (E8/vitronectin), but not feeder-based, culture. Mechanistically, we show that overexpression of MDM4, located on chromosome 1q, drives variants' advantage in E8/vitronectin by alleviating genome damage-induced apoptosis, which is lower in feeder-based conditions. Our study explains condition-dependent patterns of hPSC aberrations and offers insights into the mechanisms of variant selection.
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Affiliation(s)
- Dylan Stavish
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK; Neuroscience Institute, The University of Sheffield, Sheffield, UK; INSIGNEO Institute, The University of Sheffield, Sheffield, UK
| | - Christopher J Price
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK; Neuroscience Institute, The University of Sheffield, Sheffield, UK; INSIGNEO Institute, The University of Sheffield, Sheffield, UK
| | - Gabriele Gelezauskaite
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK; Neuroscience Institute, The University of Sheffield, Sheffield, UK; INSIGNEO Institute, The University of Sheffield, Sheffield, UK
| | - Haneen Alsehli
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK; Neuroscience Institute, The University of Sheffield, Sheffield, UK; INSIGNEO Institute, The University of Sheffield, Sheffield, UK
| | | | | | - Erik M McIntire
- WiCell Research Institute, Madison, WI, USA; Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Owen Laing
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK; Neuroscience Institute, The University of Sheffield, Sheffield, UK; INSIGNEO Institute, The University of Sheffield, Sheffield, UK
| | - Bethany M James
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK; Neuroscience Institute, The University of Sheffield, Sheffield, UK; INSIGNEO Institute, The University of Sheffield, Sheffield, UK
| | - Jack J Riley
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
| | - Johanna Zerbib
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Duncan Baker
- Sheffield Diagnostic Genetic Services, Sheffield Children's Hospital, Sheffield, UK
| | - Amy L Harding
- School of Clinical Dentistry, University of Sheffield, Sheffield, UK
| | - Lydia H Jestice
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK; Neuroscience Institute, The University of Sheffield, Sheffield, UK; INSIGNEO Institute, The University of Sheffield, Sheffield, UK
| | - Thomas F Eleveld
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Ad J M Gillis
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Sanne Hillenius
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | | | - Paul J Gokhale
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK; Neuroscience Institute, The University of Sheffield, Sheffield, UK; INSIGNEO Institute, The University of Sheffield, Sheffield, UK
| | - Uri Ben-David
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tenneille E Ludwig
- WiCell Research Institute, Madison, WI, USA; Office of the Vice Chancellor for Research and Graduate Education, University of Wisconsin-Madison, Madison, WI, USA
| | - Ivana Barbaric
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK; Neuroscience Institute, The University of Sheffield, Sheffield, UK; INSIGNEO Institute, The University of Sheffield, Sheffield, UK.
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14
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Andrews PW. The origins of human pluripotent stem cells: the road from a cancer to regenerative medicine. In Vitro Cell Dev Biol Anim 2024; 60:514-520. [PMID: 38396072 PMCID: PMC11126438 DOI: 10.1007/s11626-024-00865-8] [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: 01/15/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024]
Abstract
The notion of using pluripotent stem cells (PSCs) as a source of differentiated cell types for replacement of disease or damaged tissues in regenerative medicine is now an active area of research, with approaches to treating eye diseases such as age-related macular degeneration or Parkinson's disease now on the horizon. But the foundations for this research lie in a quite different area of science, namely the role of genetics of cancer. In this review, we trace the evolution of ideas starting with the discovery that strain 129 mice are particularly subject to develop germ cell tumors, through the identification of embryonal carcinoma (EC) cells as the stem cells of the teratocarcinoma manifestation of these tumors, to the recognition of their relationship to pluripotent cells of the early embryo, and eventually their role in the derivation of embryonic stem cells, first from mouse embryos and then from primates including humans. This is a story that illustrates how science commonly develops through the interests and insights of individual investigators, often with unexpected and unintended outcomes.
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Affiliation(s)
- Peter W Andrews
- The Centre for Stem Cell Biology, The School of Biosciences, The University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
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15
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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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16
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Krishnan S, Paul PK, Rodriguez TA. Cell competition and the regulation of protein homeostasis. Curr Opin Cell Biol 2024; 87:102323. [PMID: 38301378 DOI: 10.1016/j.ceb.2024.102323] [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: 10/18/2023] [Revised: 12/20/2023] [Accepted: 01/03/2024] [Indexed: 02/03/2024]
Abstract
The process of embryonic development involves remarkable cellular plasticity, which governs the coordination between cells necessary to build an organism. One role of this plasticity is to ensure that when aberrant cells are eliminated, growth adjustment occurs so that the size of the tissue is maintained. An important regulator of cellular plasticity that ensures cellular cooperation is a fitness-sensing mechanism termed cell competition. During cell competition, cells with defects that lower fitness but do not affect viability, such as those that cause impaired signal transduction, slower cellular growth, mitochondrial dysregulation or impaired protein homeostasis, are killed when surrounded by fitter cells. This is accompanied by the compensatory proliferation of the surviving cells. The underlying factors and mechanisms that demarcate certain cells as less fit than their neighbouring cells and losers of cell competition are still relatively unknown. Recent evidence has pointed to mitochondrial defects and proteotoxic stress as important hallmarks of these loser cells. Here, we review recent advances in this area, focussing on the role of mitochondrial activity and protein homeostasis as major mechanisms determining competitive cell fitness during development and the importance of cell proteostasis in determining cell fitness.
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Affiliation(s)
| | - Pranab K Paul
- National Heart and Lung Institute, Imperial College London, UK
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17
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Gallego Villarejo L, Gerding WM, Bachmann L, Hardt LHI, Bormann S, Nguyen HP, Müller T. Optical Genome Mapping Reveals Genomic Alterations upon Gene Editing in hiPSCs: Implications for Neural Tissue Differentiation and Brain Organoid Research. Cells 2024; 13:507. [PMID: 38534351 PMCID: PMC10969360 DOI: 10.3390/cells13060507] [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: 12/28/2023] [Revised: 03/02/2024] [Accepted: 03/05/2024] [Indexed: 03/28/2024] Open
Abstract
Genome editing, notably CRISPR (cluster regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9), has revolutionized genetic engineering allowing for precise targeted modifications. This technique's combination with human induced pluripotent stem cells (hiPSCs) is a particularly valuable tool in cerebral organoid (CO) research. In this study, CRISPR/Cas9-generated fluorescently labeled hiPSCs exhibited no significant morphological or growth rate differences compared with unedited controls. However, genomic aberrations during gene editing necessitate efficient genome integrity assessment methods. Optical genome mapping, a high-resolution genome-wide technique, revealed genomic alterations, including chromosomal copy number gain and losses affecting numerous genes. Despite these genomic alterations, hiPSCs retain their pluripotency and capacity to generate COs without major phenotypic changes but one edited cell line showed potential neuroectodermal differentiation impairment. Thus, this study highlights optical genome mapping in assessing genome integrity in CRISPR/Cas9-edited hiPSCs emphasizing the need for comprehensive integration of genomic and morphological analysis to ensure the robustness of hiPSC-based models in cerebral organoid research.
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Affiliation(s)
- Lucia Gallego Villarejo
- Department of Molecular Biochemistry, Ruhr-University Bochum, 44801 Bochum, Germany; (L.B.); (L.H.I.H.); (S.B.)
- Department of Cytology, Institute of Anatomy, Ruhr-University Bochum, 44801 Bochum, Germany
- International Graduate School of Neuroscience, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Wanda M. Gerding
- Department of Human Genetics, Ruhr-University Bochum, 44801 Bochum, Germany; (W.M.G.); (H.P.N.)
| | - Lisa Bachmann
- Department of Molecular Biochemistry, Ruhr-University Bochum, 44801 Bochum, Germany; (L.B.); (L.H.I.H.); (S.B.)
| | - Luzie H. I. Hardt
- Department of Molecular Biochemistry, Ruhr-University Bochum, 44801 Bochum, Germany; (L.B.); (L.H.I.H.); (S.B.)
| | - Stefan Bormann
- Department of Molecular Biochemistry, Ruhr-University Bochum, 44801 Bochum, Germany; (L.B.); (L.H.I.H.); (S.B.)
| | - Huu Phuc Nguyen
- Department of Human Genetics, Ruhr-University Bochum, 44801 Bochum, Germany; (W.M.G.); (H.P.N.)
| | - Thorsten Müller
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, 80336 Munich, Germany;
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18
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Arthur TD, Nguyen JP, D'Antonio-Chronowska A, Matsui H, Silva NS, Joshua IN, Luchessi AD, Greenwald WWY, D'Antonio M, Pera MF, Frazer KA. Complex regulatory networks influence pluripotent cell state transitions in human iPSCs. Nat Commun 2024; 15:1664. [PMID: 38395976 PMCID: PMC10891157 DOI: 10.1038/s41467-024-45506-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
Stem cells exist in vitro in a spectrum of interconvertible pluripotent states. Analyzing hundreds of hiPSCs derived from different individuals, we show the proportions of these pluripotent states vary considerably across lines. We discover 13 gene network modules (GNMs) and 13 regulatory network modules (RNMs), which are highly correlated with each other suggesting that the coordinated co-accessibility of regulatory elements in the RNMs likely underlie the coordinated expression of genes in the GNMs. Epigenetic analyses reveal that regulatory networks underlying self-renewal and pluripotency are more complex than previously realized. Genetic analyses identify thousands of regulatory variants that overlapped predicted transcription factor binding sites and are associated with chromatin accessibility in the hiPSCs. We show that the master regulator of pluripotency, the NANOG-OCT4 Complex, and its associated network are significantly enriched for regulatory variants with large effects, suggesting that they play a role in the varying cellular proportions of pluripotency states between hiPSCs. Our work bins tens of thousands of regulatory elements in hiPSCs into discrete regulatory networks, shows that pluripotency and self-renewal processes have a surprising level of regulatory complexity, and suggests that genetic factors may contribute to cell state transitions in human iPSC lines.
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Affiliation(s)
- Timothy D Arthur
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
- Division of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Jennifer P Nguyen
- Division of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | | | - Hiroko Matsui
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Nayara S Silva
- Northeast Biotechnology Network (RENORBIO), Graduate Program in Biotechnology, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Isaac N Joshua
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - André D Luchessi
- Northeast Biotechnology Network (RENORBIO), Graduate Program in Biotechnology, Federal University of Rio Grande do Norte, Natal, Brazil
- Department of Clinical and Toxicological Analysis, Federal University of Rio Grande do Norte, Natal, Brazil
| | - William W Young Greenwald
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Matteo D'Antonio
- Division of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | | | - Kelly A Frazer
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA.
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA.
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19
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Kim J, Kwon EJ, Kim YJ, Kim D, Shin YZ, Gil D, Kim JH, Shin HD, Kim LH, Lee MO, Go YH, Cha HJ. Epigenetic repression of CHCHD2 enhances survival from single cell dissociation through attenuated Rho A kinase activity. Cell Mol Life Sci 2024; 81:38. [PMID: 38214772 PMCID: PMC10787008 DOI: 10.1007/s00018-023-05060-8] [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: 06/14/2023] [Revised: 10/18/2023] [Accepted: 11/17/2023] [Indexed: 01/13/2024]
Abstract
During in vitro culture, human pluripotent stem cells (hPSCs) often acquire survival advantages characterized by decreased susceptibility to mitochondrial cell death, known as "culture adaptation." This adaptation is associated with genetic and epigenetic abnormalities, including TP53 mutations, copy number variations, trisomy, and methylation changes. Understanding the molecular mechanisms underlying this acquired survival advantage is crucial for safe hPSC-based cell therapies. Through transcriptome and methylome analysis, we discovered that the epigenetic repression of CHCHD2, a mitochondrial protein, is a common occurrence during in vitro culture using enzymatic dissociation. We confirmed this finding through genetic perturbation and reconstitution experiments in normal human embryonic stem cells (hESCs). Loss of CHCHD2 expression conferred resistance to single cell dissociation-induced cell death, a common stress encountered during in vitro culture. Importantly, we found that the downregulation of CHCHD2 significantly attenuates the activity of Rho-associated protein kinase (ROCK), which is responsible for inducing single cell death in hESCs. This suggests that hESCs may survive routine enzyme-based cell dissociation by downregulating CHCHD2 and thereby attenuating ROCK activity. These findings provide insights into the mechanisms by which hPSCs acquire survival advantages and adapt to in vitro culture conditions.
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Affiliation(s)
- Jumee Kim
- College of Pharmacy, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Eun-Ji Kwon
- College of Pharmacy, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Yun-Jeong Kim
- College of Pharmacy, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Dayeon Kim
- College of Pharmacy, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Yoon-Ze Shin
- College of Pharmacy, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Dayeon Gil
- Korea National Stem Cell Bank, Osong, Republic of Korea
- Division of Intractable Disease Research, Department of Chronic Disease Convergence Research, Korea National Institute of Health, Osong Health Technology Administration Complex 202, Osong, Republic of Korea
| | - Jung-Hyun Kim
- Korea National Stem Cell Bank, Osong, Republic of Korea
- Division of Intractable Disease Research, Department of Chronic Disease Convergence Research, Korea National Institute of Health, Osong Health Technology Administration Complex 202, Osong, Republic of Korea
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, Seoul, Republic of Korea
- Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea
| | - Lyoung Hyo Kim
- Research Institute for Life Science, GW Vitek, Inc., Seoul, Republic of Korea
| | - Mi-Ok Lee
- Stem Cell Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Young-Hyun Go
- College of Pharmacy, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea.
- Research Institute of Pharmaceutical Science, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea.
| | - Hyuk-Jin Cha
- College of Pharmacy, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea.
- Research Institute of Pharmaceutical Science, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea.
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20
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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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21
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Arthur TD, Nguyen JP, D'Antonio-Chronowska A, Matsui H, Silva NS, Joshua IN, Luchessi AD, Young Greenwald WW, D'Antonio M, Pera MF, Frazer KA. Analysis of regulatory network modules in hundreds of human stem cell lines reveals complex epigenetic and genetic factors contribute to pluripotency state differences between subpopulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.20.541447. [PMID: 37292794 PMCID: PMC10245835 DOI: 10.1101/2023.05.20.541447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Stem cells exist in vitro in a spectrum of interconvertible pluripotent states. Analyzing hundreds of hiPSCs derived from different individuals, we show the proportions of these pluripotent states vary considerably across lines. We discovered 13 gene network modules (GNMs) and 13 regulatory network modules (RNMs), which were highly correlated with each other suggesting that the coordinated co-accessibility of regulatory elements in the RNMs likely underlied the coordinated expression of genes in the GNMs. Epigenetic analyses revealed that regulatory networks underlying self-renewal and pluripotency have a surprising level of complexity. Genetic analyses identified thousands of regulatory variants that overlapped predicted transcription factor binding sites and were associated with chromatin accessibility in the hiPSCs. We show that the master regulator of pluripotency, the NANOG-OCT4 Complex, and its associated network were significantly enriched for regulatory variants with large effects, suggesting that they may play a role in the varying cellular proportions of pluripotency states between hiPSCs. Our work captures the coordinated activity of tens of thousands of regulatory elements in hiPSCs and bins these elements into discrete functionally characterized regulatory networks, shows that regulatory elements in pluripotency networks harbor variants with large effects, and provides a rich resource for future pluripotent stem cell research.
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22
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Barker RA, Carpenter M, Jamieson CHM, Murry CE, Pellegrini G, Rao RC, Song J. Lessons learnt, and still to learn, in first in human stem cell trials. Stem Cell Reports 2023; 18:1599-1609. [PMID: 36563687 PMCID: PMC10444539 DOI: 10.1016/j.stemcr.2022.11.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 11/15/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022] Open
Abstract
Developing cellular therapies is not straightforward. This Perspective summarizes the experience of a group of academic stem cell investigators working in different clinical areas and aims to share insight into what we wished we knew before starting. These include (1) choosing the stem cell line and assessing the genome of both the starting and final product, (2) familiarity with GMP manufacturing, reagent validation, and supply chain management, (3) product delivery issues and the additional regulatory challenges, (4) the relationship between clinical trial design and preclinical studies, and (5) the market approval requirements, pathways, and partnerships needed.
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Affiliation(s)
- Roger A Barker
- Department of Clinical Neuroscience and Wellcome-MRC Cambridge Stem Institute, John van Geest Centre for Brain Repair, Forvie Site, Robinson Way, Cambridge CB2 0QQ, UK.
| | | | - Catriona H M Jamieson
- Division of Regenerative Medicine, Department of Medicine, Sanford Stem Cell Clinical Center, University of California San Diego, Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive #0695, La Jolla, CA 92037-0695, USA
| | - Charles E Murry
- Institute for Stem Cell and Regenerative Medicine, Center for Cardiovascular Biology; Departments of Laboratory Medicine & Pathology, Bioengineering, and Medicine/Cardiology, University of Washington, Seattle, WA 98109, USA; Sana Biotechnology, Seattle, WA 98102, USA
| | - Graziella Pellegrini
- Centre for Regenerative Medicine, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Rajesh C Rao
- Departments of Ophthalmology & Visual Sciences, Pathology, and Human Genetics, University of Michigan, Surgery Service, VA Ann Arbor Health System, Ann Arbor, MI 48105, USA
| | - Jihwan Song
- Jihwan Song, Department of Biomedical Science, CHA University, 335 Pangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13488, Republic of Korea; iPS Bio, Inc., 16 Daewangpangyo-ro 712 Beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do 13488, Republic of Korea
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23
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Hejrati N, Wong R, Khazaei M, Fehlings MG. How can clinical safety and efficacy concerns in stem cell therapy for spinal cord injury be overcome? Expert Opin Biol Ther 2023; 23:883-899. [PMID: 37545020 DOI: 10.1080/14712598.2023.2245321] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 08/03/2023] [Indexed: 08/08/2023]
Abstract
INTRODUCTION Spinal cord injury (SCI) can lead to severe neurological dysfunction. Despite scientific and medical advances, clinically effective regenerative therapies including stem cells are lacking for SCI. AREAS COVERED This paper discusses translational challenges related to the safe, effective use of stem cells for SCI, with a focus on mesenchymal stem cells (MSCs), neural stem cells (NSCs), Schwann cells (SCs), olfactory ensheathing cells (OECs), oligodendrocyte precursor cells (OPCs), embryonic stem cells (ESCs), and induced pluripotent stem cells (iPSCs). We discuss approaches to enhance the efficacy of cell-based strategies by i) addressing patient heterogeneity and enhancing patient selection; ii) selecting cell type, cell source, cell developmental stage, and delivery technique; iii) enhancing graft integration and mitigating immune-mediated graft rejection; and iv) ensuring availability of cells. Additionally, we review strategies to optimize outcomes including combinatorial use of rehabilitation and discuss ways to mitigate potential risks of tumor formation associated with stem cell-based strategies. EXPERT OPINION Basic science research will drive translational advances to develop stem cell-based therapies for SCI. Genetic, serological, and imaging biomarkers may enable individualization of cell-based treatments. Moreover, combinatorial strategies will be required to enhance graft survival, migration and functional integration, to enable precision-based intervention.
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Affiliation(s)
- Nader Hejrati
- Division of Genetics and Development, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Division of Neurosurgery and Spine Program, Department of Surgery, University of Toronto, Toronto, ON, Canada
- Department of Neurosurgery & Spine Center of Eastern Switzerland, Cantonal Hospital St.Gallen, St.Gallen, Switzerland
| | - Raymond Wong
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Mohamad Khazaei
- Division of Neurosurgery and Spine Program, Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Michael G Fehlings
- Division of Genetics and Development, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Division of Neurosurgery and Spine Program, Department of Surgery, University of Toronto, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
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24
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Lai TY, Ko YC, Chen YL, Lin SF. The Way to Malignant Transformation: Can Epigenetic Alterations Be Used to Diagnose Early-Stage Head and Neck Cancer? Biomedicines 2023; 11:1717. [PMID: 37371812 PMCID: PMC10296077 DOI: 10.3390/biomedicines11061717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/05/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Identifying and treating tumors early is the key to secondary prevention in cancer control. At present, prevention of oral cancer is still challenging because the molecular drivers responsible for malignant transformation of the 11 clinically defined oral potentially malignant disorders are still unknown. In this review, we focused on studies that elucidate the epigenetic alterations demarcating malignant and nonmalignant epigenomes and prioritized findings from clinical samples. Head and neck included, the genomes of many cancer types are largely hypomethylated and accompanied by focal hypermethylation on certain specific regions. We revisited prior studies that demonstrated that sufficient uptake of folate, the primary dietary methyl donor, is associated with oral cancer reduction. As epigenetically driven phenotypic plasticity, a newly recognized hallmark of cancer, has been linked to tumor initiation, cell fate determination, and drug resistance, we discussed prior findings that might be associated with this hallmark, including gene clusters (11q13.3, 19q13.43, 20q11.2, 22q11-13) with great potential for oral cancer biomarkers, and successful examples in screening early-stage nasopharyngeal carcinoma. Although one-size-fits-all approaches have been shown to be ineffective in most cancer therapies, the rapid development of epigenome sequencing methods raises the possibility that this nonmutagenic approach may be an exception. Only time will tell.
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Affiliation(s)
- Ting-Yu Lai
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan;
- National Institute of Cancer Research, National Health Research Institutes, Miaoli 35053, Taiwan; (Y.-C.K.); (Y.-L.C.)
| | - Ying-Chieh Ko
- National Institute of Cancer Research, National Health Research Institutes, Miaoli 35053, Taiwan; (Y.-C.K.); (Y.-L.C.)
| | - Yu-Lian Chen
- National Institute of Cancer Research, National Health Research Institutes, Miaoli 35053, Taiwan; (Y.-C.K.); (Y.-L.C.)
| | - Su-Fang Lin
- National Institute of Cancer Research, National Health Research Institutes, Miaoli 35053, Taiwan; (Y.-C.K.); (Y.-L.C.)
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25
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Screening techniques to identify genomic instability of pluripotent stem cells in ensuring the safety of applications in regenerative medicine. J Stem Cells Regen Med 2023; 19:1-2. [PMID: 37366407 PMCID: PMC10290817 DOI: 10.46582/jsrm.1901001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
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26
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Skidmore S, Barker RA. Challenges in the clinical advancement of cell therapies for Parkinson's disease. Nat Biomed Eng 2023; 7:370-386. [PMID: 36635420 PMCID: PMC7615223 DOI: 10.1038/s41551-022-00987-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 11/04/2022] [Indexed: 01/14/2023]
Abstract
Cell therapies as potential treatments for Parkinson's disease first gained traction in the 1980s, owing to the clinical success of trials that used transplants of foetal midbrain dopaminergic tissue. However, the poor standardization of the tissue for grafting, and constraints on its availability and ethical use, have hindered this treatment strategy. Recent advances in stem-cell technologies and in the understanding of the development of dopaminergic neurons have enabled preclinical advancements of promising stem-cell therapies. To move these therapies to the clinic, appropriate levels of safety screening, as well as optimization of the cell products and the scalability of their manufacturing, will be required. In this Review, we discuss how challenges pertaining to cell sources, functional and safety testing, manufacturing and storage, and clinical-trial design are being addressed to advance the translational and clinical development of cell therapies for Parkinson's disease.
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Affiliation(s)
- Sophie Skidmore
- Wellcome and MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre Cambridge Biomedical Campus, Cambridge, UK
| | - Roger A Barker
- Wellcome and MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre Cambridge Biomedical Campus, Cambridge, UK.
- John van Geest Centre for Brain Repair, Department of Clinical Neuroscience, For vie Site, Cambridge, UK.
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27
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Vitillo L, Anjum F, Hewitt Z, Stavish D, Laing O, Baker D, Barbaric I, Coffey P. The isochromosome 20q abnormality of pluripotent cells interrupts germ layer differentiation. Stem Cell Reports 2023; 18:782-797. [PMID: 36801002 PMCID: PMC10031278 DOI: 10.1016/j.stemcr.2023.01.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 02/18/2023] Open
Abstract
Chromosome 20 abnormalities are some of the most frequent genomic changes acquired by human pluripotent stem cell (hPSC) cultures worldwide. Yet their effects on differentiation remain largely unexplored. We investigated a recurrent abnormality also found on amniocentesis, the isochromosome 20q (iso20q), during a clinical retinal pigment epithelium differentiation. Here we show that the iso20q abnormality interrupts spontaneous embryonic lineage specification. Isogenic lines revealed that under conditions that promote the spontaneous differentiation of wild-type hPSCs, the iso20q variants fail to differentiate into primitive germ layers and to downregulate pluripotency networks, resulting in apoptosis. Instead, iso20q cells are highly biased for extra-embryonic/amnion differentiation following inhibition of DNMT3B methylation or BMP2 treatment. Finally, directed differentiation protocols can overcome the iso20q block. Our findings reveal in iso20q a chromosomal abnormality that impairs the developmental competency of hPSCs toward germ layers but not amnion, which models embryonic developmental bottlenecks in the presence of aberrations.
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Affiliation(s)
- Loriana Vitillo
- Rescue, Repair and Regeneration, Institute of Ophthalmology, University College London, EC1V 9EL London, UK.
| | - Fabiha Anjum
- Rescue, Repair and Regeneration, Institute of Ophthalmology, University College London, EC1V 9EL London, UK
| | - Zoe Hewitt
- Centre for Stem Cell Biology, School of Biosciences, University of Sheffield, S10 2TN Sheffield, UK
| | - Dylan Stavish
- Centre for Stem Cell Biology, School of Biosciences, University of Sheffield, S10 2TN Sheffield, UK
| | - Owen Laing
- Centre for Stem Cell Biology, School of Biosciences, University of Sheffield, S10 2TN Sheffield, UK
| | - Duncan Baker
- Sheffield Diagnostic Genetic Services, Sheffield Children's Hospital, Sheffield, UK
| | - Ivana Barbaric
- Centre for Stem Cell Biology, School of Biosciences, University of Sheffield, S10 2TN Sheffield, UK
| | - Pete Coffey
- Rescue, Repair and Regeneration, Institute of Ophthalmology, University College London, EC1V 9EL London, 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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28
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TPX2 Amplification-Driven Aberrant Mitosis in Culture Adapted Human Embryonic Stem Cells with gain of 20q11.21. Stem Cell Rev Rep 2023:10.1007/s12015-023-10514-4. [PMID: 36862329 DOI: 10.1007/s12015-023-10514-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/28/2023] [Indexed: 03/03/2023]
Abstract
BACKGROUND Despite highly effective machinery for the maintenance of genome integrity in human embryonic stem cells (hESCs), the frequency of genetic aberrations during in-vitro culture has been a serious issue for future clinical applications. METHOD By passaging hESCs over a broad range of timepoints (up to 6 years), the isogenic hESC lines with different passage numbers with distinct cellular characteristics, were established. RESULT We found that mitotic aberrations, such as the delay of mitosis, multipolar centrosomes, and chromosome mis-segregation, were increased in parallel with polyploidy compared to early-passaged hESCs (EP-hESCs) with normal copy number. Through high-resolution genome-wide approaches and transcriptome analysis, we found that culture adapted-hESCs with a minimal amplicon in chromosome 20q11.21 highly expressed TPX2, a key protein for governing spindle assembly and cancer malignancy. Consistent with these findings, the inducible expression of TPX2 in EP-hESCs reproduced aberrant mitotic events, such as the delay of mitotic progression, spindle stabilization, misaligned chromosomes, and polyploidy. CONCLUSION These studies suggest that the increased transcription of TPX2 in culture adapted hESCs could contribute to an increase in aberrant mitosis due to altered spindle dynamics.
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29
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Cichocki F, van der Stegen SJC, Miller JS. Engineered and banked iPSCs for advanced NK- and T-cell immunotherapies. Blood 2023; 141:846-855. [PMID: 36327161 PMCID: PMC10023718 DOI: 10.1182/blood.2022016205] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/11/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
The development of methods to derive induced pluripotent stem cells (iPSCs) has propelled stem cell research, and has the potential to revolutionize many areas of medicine, including cancer immunotherapy. These cells can be propagated limitlessly and can differentiate into nearly any specialized cell type. The ability to perform precise multigene engineering at the iPSC stage, generate master cell lines after clonal selection, and faithfully promote differentiation along natural killer (NK) cells and T-cell lineages is now leading to new opportunities for the administration of off-the-shelf cytotoxic lymphocytes with direct antigen targeting to treat patients with relapsed/refractory cancer. In this review, we highlight the recent progress in iPSC editing and guided differentiation in the development of NK- and T-cell products for immunotherapy. We also discuss some of the potential barriers that remain in unleashing the full potential of iPSC-derived cytotoxic effector cells in the adoptive transfer setting, and how some of these limitations may be overcome through gene editing.
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Affiliation(s)
- Frank Cichocki
- Department of Medicine, University of Minnesota, Minneapolis, MN
| | - Sjoukje J. C. van der Stegen
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY
- Immunology Program, Sloan Kettering Institute, New York, NY
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30
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Kim YJ, Go YH, Jeong HC, Kwon EJ, Kim SM, Cheong HS, Kim W, Shin HD, Lee H, Cha HJ. TPX2 prompts mitotic survival via the induction of BCL2L1 through YAP1 protein stabilization in human embryonic stem cells. Exp Mol Med 2023; 55:32-42. [PMID: 36596852 PMCID: PMC9898288 DOI: 10.1038/s12276-022-00907-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 10/07/2022] [Accepted: 10/31/2022] [Indexed: 01/05/2023] Open
Abstract
Genetic alterations have been reported for decades in most human embryonic stem cells (hESCs). Survival advantage, a typical trait acquired during long-term in vitro culture, results from the induction of BCL2L1 upon frequent copy number variation (CNV) at locus 20q11.21 and is one of the strongest candidates associated with genetic alterations that occur via escape from mitotic stress. However, the underlying mechanisms for BCL2L1 induction remain unknown. Furthermore, abnormal mitosis and the survival advantage that frequently occur in late passage are associated with the expression of BCL2L1, which is in locus 20q11.21. In this study, we demonstrated that the expression of TPX2, a gene located in 20q11.21, led to BCL2L1 induction and consequent survival traits under mitotic stress in isogenic pairs of hESCs and human induced pluripotent stem cells (iPSCs) with normal and 20q11.21 CNVs. High Aurora A kinase activity by TPX2 stabilized the YAP1 protein to induce YAP1-dependent BCL2L1 expression. A chemical inhibitor of Aurora A kinase and knockdown of YAP/TAZ significantly abrogated the high tolerance to mitotic stress through BCL2L1 suppression. These results suggest that the collective expression of TPX2 and BCL2L1 from CNV at loci 20q11.21 and a consequent increase in YAP1 signaling promote genome instability during long-term in vitro hESC culture.
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Affiliation(s)
- Yun-Jeong Kim
- grid.31501.360000 0004 0470 5905College of Pharmacy, Seoul National University, Seoul, 08826 Republic of Korea
| | - Young-Hyun Go
- grid.263736.50000 0001 0286 5954Department of Life Sciences, Sogang University, Seoul, 04107 Republic of Korea
| | - Ho-Chang Jeong
- grid.263736.50000 0001 0286 5954Department of Life Sciences, Sogang University, Seoul, 04107 Republic of Korea
| | - Eun-Ji Kwon
- grid.31501.360000 0004 0470 5905College of Pharmacy, Seoul National University, Seoul, 08826 Republic of Korea
| | - Seong-Min Kim
- grid.31501.360000 0004 0470 5905College of Pharmacy, Seoul National University, Seoul, 08826 Republic of Korea
| | - Hyun Sub Cheong
- grid.412670.60000 0001 0729 3748Drug Information Research Institute, College of Pharmacy, Sookmyung Women’s University, Seoul, 04310 Republic of Korea
| | - Wantae Kim
- grid.254230.20000 0001 0722 6377Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Hyoung Doo Shin
- grid.263736.50000 0001 0286 5954Department of Life Sciences, Sogang University, Seoul, 04107 Republic of Korea
| | - Haeseung Lee
- grid.262229.f0000 0001 0719 8572College of Pharmacy, Pusan National University, Busan, 46241 Korea
| | - Hyuk-Jin Cha
- College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
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31
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Andrews PW, Barbaric I, Benvenisty N, Draper JS, Ludwig T, Merkle FT, Sato Y, Spits C, Stacey GN, Wang H, Pera MF. The consequences of recurrent genetic and epigenetic variants in human pluripotent stem cells. Cell Stem Cell 2022; 29:1624-1636. [PMID: 36459966 DOI: 10.1016/j.stem.2022.11.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/08/2022] [Accepted: 11/08/2022] [Indexed: 12/05/2022]
Abstract
It is well established that human pluripotent stem cells (hPSCs) can acquire genetic and epigenetic changes during culture in vitro. Given the increasing use of hPSCs in research and therapy and the vast expansion in the number of hPSC lines available for researchers, the International Society for Stem Cell Research has recognized the need to reassess quality control standards for ensuring the genetic integrity of hPSCs. Here, we summarize current knowledge of the nature of recurrent genetic and epigenetic variants in hPSC culture, the methods for their detection, and what is known concerning their effects on cell behavior in vitro or in vivo. We argue that the potential consequences of low-level contamination of cell therapy products with cells bearing oncogenic variants are essentially unknown at present. We highlight the key challenges facing the field with particular reference to safety assessment of hPSC-derived cellular therapeutics.
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Affiliation(s)
- Peter W Andrews
- Centre for Stem Cell Biology, School of Biological Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK; Steering Committee, International Stem Cell Initiative
| | - Ivana Barbaric
- Centre for Stem Cell Biology, School of Biological Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK; Steering Committee, International Stem Cell Initiative
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel; Steering Committee, International Stem Cell Initiative
| | - Jonathan S Draper
- Stem Cell Network, 501 Smyth Road, Ottawa, ON, K1H 8L6, Canada; Steering Committee, International Stem Cell Initiative
| | - Tenneille Ludwig
- WiCell Research Institute, Madison, WI, USA; University of Wisconsin-Madison, Madison, WI 53719, USA; Steering Committee, International Stem Cell Initiative
| | - Florian T Merkle
- Wellcome Trust-Medical Research Council Institute of Metabolic Science, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0QQ, UK; Steering Committee, International Stem Cell Initiative
| | - Yoji Sato
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki Ward, Kawasaki City, Kanagawa 210-9501, Japan; Steering Committee, International Stem Cell Initiative
| | - Claudia Spits
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium; Steering Committee, International Stem Cell Initiative
| | - Glyn N Stacey
- International Stem Cell Banking Initiative, 2 High Street, Barley, UK; National Stem Cell Resource Centre, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100190, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China; Steering Committee, International Stem Cell Initiative
| | - Haoyi Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China; Beijing Institute for Stem Cell and Regenerative Medicine, 100101, Beijing, China; Steering Committee, International Stem Cell Initiative
| | - Martin F Pera
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA; Steering Committee, International Stem Cell Initiative.
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32
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Steventon-Jones V, Stavish D, Halliwell JA, Baker D, Barbaric I. Single Nucleotide Polymorphism (SNP) Arrays and Their Sensitivity for Detection of Genetic Changes in Human Pluripotent Stem Cell Cultures. Curr Protoc 2022; 2:e606. [PMID: 36426882 DOI: 10.1002/cpz1.606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Human pluripotent stem cells (hPSCs) can be grown in culture indefinitely, making them a valuable tool for use in basic biology, disease modeling, and regenerative medicine. However, over prolonged periods in culture, hPSCs tend to acquire genomic aberrations that confer growth advantages, similar to those seen in some cancers. Monitoring the genomic stability of cultured hPSCs is critical to ensuring their efficacy and safety as a therapeutic tool. Most commonly employed methods for monitoring of hPSC genomes are cytogenetic methods, such as G-banding. Nonetheless, such methods have limited resolution and sensitivity for detecting mosaicism. Single nucleotide polymorphism (SNP) array platforms are a potential alternative that could improve detection of abnormalities. Here, we outline protocols for SNP array whole-genome screening of hPSCs. Moreover, we detail the procedure for assessing the SNP array's sensitivity in detecting low-level mosaic copy-number changes. We show that mosaicism can be confidently identified in samples only once they contain 20% variants, although samples containing 10% variants typically display enough variation to warrant further investigation and confirmation, for example by using a more sensitive targeted method. Finally, we highlight the advantages and limitations of SNP arrays, including a cost comparison of SNP arrays versus other commonly employed methods for detection of genetic changes in hPSC cultures. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: DNA sample preparation for SNP arrays Basic Protocol 2: SNP array hybridization, washing, and scanning Basic Protocol 3: SNP array data analysis Support Protocol: Assessment of SNP array sensitivity for detection of mosaicism.
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Affiliation(s)
| | - Dylan Stavish
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Western Bank, Sheffield, United Kingdom.,Neuroscience Institute, The University of Sheffield, Western Bank, Sheffield, United Kingdom
| | - Jason A Halliwell
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Western Bank, Sheffield, United Kingdom.,Neuroscience Institute, The University of Sheffield, Western Bank, Sheffield, United Kingdom.,Current address: Center for Chromosome Stability, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, Copenhagen, Denmark
| | - Duncan Baker
- Sheffield Diagnostic Genetic Services, Sheffield Children's Hospital, Sheffield, United Kingdom
| | - Ivana Barbaric
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Western Bank, Sheffield, United Kingdom.,Neuroscience Institute, The University of Sheffield, Western Bank, Sheffield, United Kingdom
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33
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Rouhani FJ, Zou X, Danecek P, Badja C, Amarante TD, Koh G, Wu Q, Memari Y, Durbin R, Martincorena I, Bassett AR, Gaffney D, Nik-Zainal S. Substantial somatic genomic variation and selection for BCOR mutations in human induced pluripotent stem cells. Nat Genet 2022; 54:1406-1416. [PMID: 35953586 PMCID: PMC9470532 DOI: 10.1038/s41588-022-01147-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/24/2022] [Indexed: 12/27/2022]
Abstract
We explored human induced pluripotent stem cells (hiPSCs) derived from different tissues to gain insights into genomic integrity at single-nucleotide resolution. We used genome sequencing data from two large hiPSC repositories involving 696 hiPSCs and daughter subclones. We find ultraviolet light (UV)-related damage in ~72% of skin fibroblast-derived hiPSCs (F-hiPSCs), occasionally resulting in substantial mutagenesis (up to 15 mutations per megabase). We demonstrate remarkable genomic heterogeneity between independent F-hiPSC clones derived during the same round of reprogramming due to oligoclonal fibroblast populations. In contrast, blood-derived hiPSCs (B-hiPSCs) had fewer mutations and no UV damage but a high prevalence of acquired BCOR mutations (26.9% of lines). We reveal strong selection pressure for BCOR mutations in F-hiPSCs and B-hiPSCs and provide evidence that they arise in vitro. Directed differentiation of hiPSCs and RNA sequencing showed that BCOR mutations have functional consequences. Our work strongly suggests that detailed nucleotide-resolution characterization is essential before using hiPSCs.
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Affiliation(s)
- Foad J Rouhani
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Xueqing Zou
- Early Cancer Institute, Hutchison/MRC Research Centre, Cambridge Biomedical Research Campus, Cambridge, UK
- Academic Department of Medical Genetics, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge, UK
| | - Petr Danecek
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Cherif Badja
- Early Cancer Institute, Hutchison/MRC Research Centre, Cambridge Biomedical Research Campus, Cambridge, UK
- Academic Department of Medical Genetics, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge, UK
| | - Tauanne Dias Amarante
- Early Cancer Institute, Hutchison/MRC Research Centre, Cambridge Biomedical Research Campus, Cambridge, UK
| | - Gene Koh
- Early Cancer Institute, Hutchison/MRC Research Centre, Cambridge Biomedical Research Campus, Cambridge, UK
- Academic Department of Medical Genetics, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge, UK
| | - Qianxin Wu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yasin Memari
- Early Cancer Institute, Hutchison/MRC Research Centre, Cambridge Biomedical Research Campus, Cambridge, UK
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Inigo Martincorena
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Andrew R Bassett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Daniel Gaffney
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Genomics plc, King Charles House, Oxford, UK
| | - Serena Nik-Zainal
- Early Cancer Institute, Hutchison/MRC Research Centre, Cambridge Biomedical Research Campus, Cambridge, UK.
- Academic Department of Medical Genetics, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge, UK.
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34
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Molina-Ruiz FJ, Introna C, Bombau G, Galofre M, Canals JM. Standardization of Cell Culture Conditions and Routine Genomic Screening under a Quality Management System Leads to Reduced Genomic Instability in hPSCs. Cells 2022; 11:cells11131984. [PMID: 35805069 PMCID: PMC9265327 DOI: 10.3390/cells11131984] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/11/2022] [Accepted: 06/13/2022] [Indexed: 01/27/2023] Open
Abstract
Human pluripotent stem cells (hPSCs) have generated unprecedented interest in the scientific community, given their potential applications in regenerative medicine, disease modeling, toxicology and drug screening. However, hPSCs are prone to acquire genomic alterations in vitro, mainly due to suboptimal culture conditions and inappropriate routines to monitor genome integrity. This poses a challenge to both the safety of clinical applications and the reliability of basic and translational hPSC research. In this study, we aim to investigate if the implementation of a Quality Management System (QMS) such as ISO9001:2015 to ensure reproducible and standardized cell culture conditions and genomic screening strategies can decrease the prevalence of genomic alterations affecting hPSCs used for research applications. To this aim, we performed a retrospective analysis of G-banding karyotype and Comparative Genomic Hybridization array (aCGH) data generated by our group over a 5-year span of different hESC and hiPSC cultures. This work demonstrates that application of a QMS to standardize cell culture conditions and genomic monitoring routines leads to a striking improvement of genomic stability in hPSCs cultured in vitro, as evidenced by a reduced probability of potentially pathogenic chromosomal aberrations and subchromosomal genomic alterations. These results support the need to implement QMS in academic laboratories performing hPSC research.
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Affiliation(s)
- Francisco J. Molina-Ruiz
- Laboratory of Stem Cells and Regenerative Medicine, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain; (F.J.M.-R.); (C.I.); (G.B.); (M.G.)
- Creatio, Production and Validation Center of Advanced Therapies, Faculty of Medicine and Health Science, University of Barcelona, 08036 Barcelona, Spain
- Institute of Neurosciences, University of Barcelona, 08036 Barcelona, Spain
- Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), 08036 Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
| | - Clelia Introna
- Laboratory of Stem Cells and Regenerative Medicine, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain; (F.J.M.-R.); (C.I.); (G.B.); (M.G.)
- Creatio, Production and Validation Center of Advanced Therapies, Faculty of Medicine and Health Science, University of Barcelona, 08036 Barcelona, Spain
- Institute of Neurosciences, University of Barcelona, 08036 Barcelona, Spain
- Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), 08036 Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
| | - Georgina Bombau
- Laboratory of Stem Cells and Regenerative Medicine, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain; (F.J.M.-R.); (C.I.); (G.B.); (M.G.)
- Creatio, Production and Validation Center of Advanced Therapies, Faculty of Medicine and Health Science, University of Barcelona, 08036 Barcelona, Spain
- Institute of Neurosciences, University of Barcelona, 08036 Barcelona, Spain
- Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), 08036 Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
| | - Mireia Galofre
- Laboratory of Stem Cells and Regenerative Medicine, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain; (F.J.M.-R.); (C.I.); (G.B.); (M.G.)
- Creatio, Production and Validation Center of Advanced Therapies, Faculty of Medicine and Health Science, University of Barcelona, 08036 Barcelona, Spain
- Institute of Neurosciences, University of Barcelona, 08036 Barcelona, Spain
- Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), 08036 Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
| | - Josep M. Canals
- Laboratory of Stem Cells and Regenerative Medicine, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain; (F.J.M.-R.); (C.I.); (G.B.); (M.G.)
- Creatio, Production and Validation Center of Advanced Therapies, Faculty of Medicine and Health Science, University of Barcelona, 08036 Barcelona, Spain
- Institute of Neurosciences, University of Barcelona, 08036 Barcelona, Spain
- Networked Biomedical Research Centre for Neurodegenerative Disorders (CIBERNED), 08036 Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
- Correspondence: ; Tel.: +34-934-035-288
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35
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Lezmi E, Benvenisty N. The Tumorigenic Potential of Human Pluripotent Stem Cells. Stem Cells Transl Med 2022; 11:791-796. [PMID: 35679163 PMCID: PMC9397652 DOI: 10.1093/stcltm/szac039] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/24/2022] [Indexed: 11/23/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) are currently evaluated for clinical applications due to their proliferation and differentiation capacities, raising the need to both assess and enhance, the safety of hPSC-based treatments. Distinct molecular features contribute to the tumorigenicity of hPSCs, manifested in the formation of teratoma tumors upon transplantation in vivo. Prolonged in vitro culturing of hPSCs can enhance selection for specific genetic aberrations, either at the chromosome or gene level. Some of these aberrations are tightly linked to human tumor pathology and increase the tumorigenic aggressiveness of the abnormal cells. In this perspective, we describe major tumor-associated risk factors entailed in hPSC-based therapy, and present precautionary and safety measures relevant for the development and application of such therapies.
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Affiliation(s)
- Elyad Lezmi
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel
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36
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Morita Y, Kishino Y, Fukuda K, Tohyama S. Scalable manufacturing of clinical-grade differentiated cardiomyocytes derived from human-induced pluripotent stem cells for regenerative therapy. Cell Prolif 2022; 55:e13248. [PMID: 35534945 PMCID: PMC9357358 DOI: 10.1111/cpr.13248] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 04/14/2022] [Accepted: 04/19/2022] [Indexed: 12/17/2022] Open
Abstract
Basic research on human pluripotent stem cell (hPSC)‐derived cardiomyocytes (CMs) for cardiac regenerative therapy is one of the most active and complex fields to achieve this alternative to heart transplantation and requires the integration of medicine, science, and engineering. Mortality in patients with heart failure remains high worldwide. Although heart transplantation is the sole strategy for treating severe heart failure, the number of donors is limited. Therefore, hPSC‐derived CM (hPSC‐CM) transplantation is expected to replace heart transplantation. To achieve this goal, for basic research, various issues should be considered, including how to induce hPSC proliferation efficiently for cardiac differentiation, induce hPSC‐CMs, eliminate residual undifferentiated hPSCs and non‐CMs, and assess for the presence of residual undifferentiated hPSCs in vitro and in vivo. In this review, we discuss the current stage of resolving these issues and future directions for realizing hPSC‐based cardiac regenerative therapy.
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Affiliation(s)
- Yuika Morita
- Department of Cardiology, Keio University School of Medicine, Tokyo, Japan
| | - Yoshikazu Kishino
- Department of Cardiology, Keio University School of Medicine, Tokyo, Japan
| | - Keiichi Fukuda
- Department of Cardiology, Keio University School of Medicine, Tokyo, Japan
| | - Shugo Tohyama
- Department of Cardiology, Keio University School of Medicine, Tokyo, Japan
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37
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Akutsu SN, Miyamoto T, Oba D, Tomioka K, Ochiai H, Ohashi H, Matsuura S. iPSC reprogramming-mediated aneuploidy correction in autosomal trisomy syndromes. PLoS One 2022; 17:e0264965. [PMID: 35271616 PMCID: PMC8912248 DOI: 10.1371/journal.pone.0264965] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 01/25/2022] [Indexed: 12/25/2022] Open
Abstract
Trisomy 21, 18, and 13 are the major autosomal aneuploidy disorders in humans. They are mostly derived from chromosome non-disjunction in maternal meiosis, and the extra trisomic chromosome can cause several congenital malformations. Various genes on the trisomic chromosomes are intricately involved in the development of disease, and fundamental treatments have not yet been established. However, chromosome therapy has been developed to correct the extra chromosome in cultured patient cells, and it was recently reported that during reprogramming into iPSCs, fibroblasts from a Down syndrome patient lost the extra chromosome 21 due to a phenomenon called trisomy-biased chromosome loss. To gain preliminary insights into the underlying mechanism of trisomy rescue during the early stages of reprogramming, we reprogrammed skin fibroblasts from patients with trisomy syndromes 21, 18, 13, and 9 to iPSC, and evaluated the genomes of the individual iPSC colonies by molecular cytogenetic techniques. We report the spontaneous correction from trisomy to disomy upon cell reprogramming in at least one cell line examined from each of the trisomy syndromes, and three possible combinations of chromosomes were selected in the isogenic trisomy-rescued iPSC clones. Single nucleotide polymorphism analysis showed that the trisomy-rescued clones exhibited either heterodisomy or segmental uniparental isodisomy, ruling out the possibility that two trisomic chromosomes were lost simultaneously and the remaining one was duplicated, suggesting instead that one trisomic chromosome was lost to generate disomic cells. These results demonstrated that trisomy rescue may be a phenomenon with random loss of the extra chromosome and subsequent selection for disomic iPSCs, which is analogous to the karyotype correction in early preimplantation embryos. Our finding is relevant for elucidating the mechanisms of autonomous karyotype correction and future application in basic and clinical research on aneuploidy disorders.
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Affiliation(s)
- Silvia Natsuko Akutsu
- Department of Genetics and Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Tatsuo Miyamoto
- Department of Genetics and Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Daiju Oba
- Department of Genetics, Saitama Children’s Medical Center, Saitama, Japan
| | - Keita Tomioka
- Department of Genetics and Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
- Department of Pediatrics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hiroshi Ochiai
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Hirofumi Ohashi
- Department of Genetics, Saitama Children’s Medical Center, Saitama, Japan
| | - Shinya Matsuura
- Department of Genetics and Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
- * E-mail:
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38
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Basundra R, Kapoor S, Hollville E, Kiapour N, Beltran Lopez A, Marie Melchiorre N, Deshmukh M. Constitutive High Expression of NOXA Sensitizes Human Embryonic Stem Cells for Rapid Cell Death. Stem Cells 2022; 40:49-58. [PMID: 35511861 PMCID: PMC9199843 DOI: 10.1093/stmcls/sxab008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 09/02/2021] [Indexed: 01/21/2023]
Abstract
Human embryonic stem (hES) cells are highly sensitive to apoptotic stimuli such as DNA damage, which allows for the rapid elimination of mutated cells during development. However, the mechanisms that maintain hES cells in the primed apoptotic state are not completely known. Key activators of apoptosis, the BH3-only proteins, are present at low levels in most cell types. In contrast, hES cells have constitutive high levels of the BH3-only protein, NOXA. We examined the importance of NOXA for enabling apoptosis in hES cells. hES cells deleted for NOXA showed remarkable protection against multiple apoptotic stimuli. NOXA was constitutively localized to the mitochondria, where it interacted with MCL1. Strikingly, inhibition of MCL1 in NOXA knockout cells was sufficient to sensitize these cells to DNA damage-induced cell death. Our study demonstrates that an essential function of constitutive high levels of NOXA in hES cells is to effectively antagonize MCL1 to permit rapid apoptosis.
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Affiliation(s)
- Richa Basundra
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA
| | - Sahil Kapoor
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA
| | - Emilie Hollville
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA
| | - Nazanin Kiapour
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA
| | - Adriana Beltran Lopez
- Human Pluripotent Stem Cell Core, Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | | | - Mohanish Deshmukh
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA
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39
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Merkle FT, Ghosh S, Genovese G, Handsaker RE, Kashin S, Meyer D, Karczewski KJ, O'Dushlaine C, Pato C, Pato M, MacArthur DG, McCarroll SA, Eggan K. Whole-genome analysis of human embryonic stem cells enables rational line selection based on genetic variation. Cell Stem Cell 2022; 29:472-486.e7. [PMID: 35176222 PMCID: PMC8900618 DOI: 10.1016/j.stem.2022.01.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 10/29/2021] [Accepted: 01/24/2022] [Indexed: 02/02/2023]
Abstract
Despite their widespread use in research, there has not yet been a systematic genomic analysis of human embryonic stem cell (hESC) lines at a single-nucleotide resolution. We therefore performed whole-genome sequencing (WGS) of 143 hESC lines and annotated their single-nucleotide and structural genetic variants. We found that while a substantial fraction of hESC lines contained large deleterious structural variants, finer-scale structural and single-nucleotide variants (SNVs) that are ascertainable only through WGS analyses were present in hESC genomes and human blood-derived genomes at similar frequencies. Moreover, WGS allowed us to identify SNVs associated with cancer and other diseases that could alter cellular phenotypes and compromise the safety of hESC-derived cellular products transplanted into humans. As a resource to enable reproducible hESC research and safer translation, we provide a user-friendly WGS data portal and a data-driven scheme for cell line maintenance and selection.
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Affiliation(s)
- Florian T Merkle
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Wellcome - MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK; Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK.
| | - Sulagna Ghosh
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Giulio Genovese
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Robert E Handsaker
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Seva Kashin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel Meyer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Konrad J Karczewski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Colm O'Dushlaine
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carlos Pato
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA; Department of Psychiatry, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Michele Pato
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA; Department of Psychiatry, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Daniel G MacArthur
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, NSW, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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40
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Takahashi K, Okubo C, Nakamura M, Iwasaki M, Kawahara Y, Tabata T, Miyamoto Y, Woltjen K, Yamanaka S. A stress-reduced passaging technique improves the viability of human pluripotent cells. CELL REPORTS METHODS 2022; 2:100155. [PMID: 35474962 PMCID: PMC9017214 DOI: 10.1016/j.crmeth.2021.100155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/13/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
Xeno-free culture systems have expanded the clinical and industrial application of human pluripotent stem cells (PSCs). However, reproducibility issues, often arising from variability during passaging steps, remain. Here, we describe an improved method for the subculture of human PSCs. The revised method significantly enhances the viability of human PSCs by lowering DNA damage and apoptosis, resulting in more efficient and reproducible downstream applications such as gene editing and directed differentiation. Furthermore, the method does not alter PSC characteristics after long-term culture and attenuates the growth advantage of abnormal subpopulations. This robust passaging method minimizes experimental error and reduces the rate of PSCs failing quality control of human PSC research and application.
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Affiliation(s)
- Kazutoshi Takahashi
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Chikako Okubo
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Michiko Nakamura
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Mio Iwasaki
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Yuka Kawahara
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Tsuyoshi Tabata
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Yousuke Miyamoto
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Knut Woltjen
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Shinya Yamanaka
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
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41
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Baker D, Barbaric I. Characterizing the Genetic Stability of Human Naïve and Primed Pluripotent Stem Cells. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2416:267-284. [PMID: 34870842 DOI: 10.1007/978-1-0716-1908-7_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The presence of genetic changes in human pluripotent stem cells (hPSCs) can affect their behavior and impact on the utility of hPSC-based applications in research and clinic. The spectrum of spontaneously arising genetic abnormalities in hPSCs is wide and ranges from numerical and structural chromosomal anomalies down to point mutations. The detection of genetic changes in hPSCs is confounded by the fact that no single method detects all types of abnormalities with the same accuracy and sensitivity, therefore necessitating the use of a combination of different methods. Here, we provide detailed protocols for two methods commonly utilized for the detection of genetic changes in naïve and primed hPSCs: karyotyping by G-banding and fluorescent in situ hybridization (FISH).
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Affiliation(s)
- Duncan Baker
- Sheffield Diagnostic Genetic Services, Sheffield Children's Hospital, Sheffield, UK
| | - Ivana Barbaric
- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Western Bank, Sheffield, UK.
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42
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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: 1.3] [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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43
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Affiliation(s)
- Seungbok Yang
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Yoonjae Cho
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Jiwon Jang
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
- Institute of Convergence Science, Yonsei University, Seoul 03722, Korea
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44
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Price CJ, Stavish D, Gokhale PJ, Stevenson BA, Sargeant S, Lacey J, Rodriguez TA, Barbaric I. Genetically variant human pluripotent stem cells selectively eliminate wild-type counterparts through YAP-mediated cell competition. Dev Cell 2021; 56:2455-2470.e10. [PMID: 34407428 PMCID: PMC8443275 DOI: 10.1016/j.devcel.2021.07.019] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 05/09/2021] [Accepted: 07/26/2021] [Indexed: 12/21/2022]
Abstract
The appearance of genetic changes in human pluripotent stem cells (hPSCs) presents a concern for their use in research and regenerative medicine. Variant hPSCs that harbor recurrent culture-acquired aneuploidies display growth advantages over wild-type diploid cells, but the mechanisms that yield a drift from predominantly wild-type to variant cell populations remain poorly understood. Here, we show that the dominance of variant clones in mosaic cultures is enhanced through competitive interactions that result in the elimination of wild-type cells. This elimination occurs through corralling and mechanical compression by faster-growing variants, causing a redistribution of F-actin and sequestration of yes-associated protein (YAP) in the cytoplasm that induces apoptosis in wild-type cells. YAP overexpression or promotion of YAP nuclear localization in wild-type cells alleviates their "loser" phenotype. Our results demonstrate that hPSC fate is coupled to mechanical cues imposed by neighboring cells and reveal that hijacking this mechanism allows variants to achieve clonal dominance in cultures.
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Affiliation(s)
- Christopher J Price
- Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield S10 2TN, UK; Neuroscience Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Dylan Stavish
- Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield S10 2TN, UK; Neuroscience Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Paul J Gokhale
- Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Ben A Stevenson
- Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Samantha Sargeant
- Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield S10 2TN, UK; Department of Automatic Control and Systems Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, UK
| | - Joanne Lacey
- Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Tristan A Rodriguez
- National Heart and Lung Institute, Imperial Centre for Translational and Experimental Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Ivana Barbaric
- Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield S10 2TN, UK; Neuroscience Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, UK.
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45
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Wu J, Barbaric I. Fitness selection in human pluripotent stem cells and interspecies chimeras: Implications for human development and regenerative medicine. Dev Biol 2021; 476:209-217. [PMID: 33891964 PMCID: PMC8209287 DOI: 10.1016/j.ydbio.2021.03.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/25/2021] [Accepted: 03/30/2021] [Indexed: 12/12/2022]
Abstract
A small number of pluripotent cells within early embryo gives rise to all cells in the adult body, including germ cells. Hence, any mutations occurring in the pluripotent cell population are at risk of being propagated to their daughter cells and could lead to congenital defects or embryonic lethality and pose a risk of being transmitted to future generations. The observation that genetic errors are relatively common in preimplantation embryos, but their levels reduce as development progresses, suggests the existence of mechanisms for clearance of aberrant, unfit or damaged cells. Although early human embryogenesis is largely experimentally inaccessible, pluripotent stem cell (PSC) lines can be derived either from the inner cell mass (ICM) of a blastocyst or by reprogramming somatic cells into an embryonic stem cell-like state. PSCs retain the ability to differentiate into any cell type in vitro and, hence, they represent a unique and powerful tool for studying otherwise intractable stages of human development. The advent of PSCs has also opened up a possibility of developing regenerative medicine therapies, either through PSC differentiation in vitro or by creating interspecies chimeras for organ replacement. Here, we discuss the emerging evidence of cell selection in human PSC populations in vivo and in vitro and we highlight the implications of understanding this phenomenon for human development and regenerative medicine.
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Affiliation(s)
- Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Ivana Barbaric
- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom; Neuroscience Institute, The University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom.
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46
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Riggs MJ, Sheridan SD, Rao RR. ARHGDIA Confers Selective Advantage to Dissociated Human Pluripotent Stem Cells. Stem Cells Dev 2021; 30:705-713. [PMID: 34036793 PMCID: PMC8309423 DOI: 10.1089/scd.2021.0079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) have generated significant interest in the scientific community based on their potential applications in regenerative medicine. However, numerous research groups have reported a propensity for genomic alterations during hPSC culture that poses concerns for basic research and clinical applications. Work from our laboratory and others has demonstrated that amplification of chromosomal regions is correlated with increased gene expression. To date, the phenotypic association of common genomic alterations remains unclear and is a cause for concern during clinical use. In this study, we focus on trisomy 17 and a list of candidate genes with increased gene expression to hypothesize that overexpressing 17q25 located ARHGDIA will confer selective advantage to hPSCs. HPSC lines overexpressing ARHGDIA exhibited culture dominance in co-cultures of overexpression lines with nonoverexpression lines. Furthermore, during low-density seeding, we demonstrate increased clonality of our ARHGDIA lines against matched controls. A striking observation is that we could reduce this selective advantage by varying the hPSC culture conditions with the addition of ROCK inhibitor (ROCKi). This work is unique in (1) demonstrating a novel gene that confers selective advantage to hPSCs when overexpressed and may help explain a common trisomy dominance, (2) providing a selection model for studying culture conditions that reduce the appearance of genomically altered hPSCs, and (3) aiding in elucidation of a mechanism that may act as a molecular switch during culture adaptation.
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Affiliation(s)
- Marion J Riggs
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, Virginia, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Neurology, Harvard Medical School, Boston, Massachusetts, USA
| | - Steven D Sheridan
- Center for Quantitative Health, Center for Genomic Medicine and Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Psychiatry, Harvard Medical School, Boston, Massachusetts, USA
| | - Raj R Rao
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, Virginia, USA.,Department of Biomedical Engineering, College of Engineering, University of Arkansas, Fayetteville, Arkansas, USA
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47
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McIntire E, Taapken S, Leonhard K, Larson AL. Genomic Stability Testing of Pluripotent Stem Cells. ACTA ACUST UNITED AC 2021; 52:e107. [PMID: 32105415 DOI: 10.1002/cpsc.107] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Pluripotent stem cell (PSC) cultures are subjected to selective pressures that can result in acquisition and expansion of recurrent genetic abnormalities at any time. These recurrent abnormalities enhance the variant cells harboring them with a competitive advantage over wild-type cells. Variant cells can eventually supplant wild-type cells entirely and become fixed in culture. Such variants can impact the efficacy of PSCs in research and clinical applications. Therefore, routine genomic characterization is required for reliable and effective use of PSCs. In this article we describe the capabilities and limitations of several assays commonly used for assessing PSC genomic stability. Based on this analysis, we provide a recommendation for integrating assays into a comprehensive testing regimen that maximizes coverage while minimizing cost. © 2020 by John Wiley & Sons, Inc.
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48
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Halliwell JA, Gravells P, Bryant HE. DNA Fiber Assay for the Analysis of DNA Replication Progression in Human Pluripotent Stem Cells. ACTA ACUST UNITED AC 2021; 54:e115. [PMID: 32584505 DOI: 10.1002/cpsc.115] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Human pluripotent stem cells (PSC) acquire recurrent chromosomal instabilities during prolonged in vitro culture that threaten to preclude their use in cell-based regenerative medicine. The rapid proliferation of pluripotent cells leads to constitutive replication stress, hindering the progression of DNA replication forks and in some cases leading to replication-fork collapse. Failure to overcome replication stress can result in incomplete genome duplication, which, if left to persist into the subsequent mitosis, can result in structural and numerical chromosomal instability. We have recently applied the DNA fiber assay to the study of replication stress in human PSC and found that, in comparison to somatic cells states, these cells display features of DNA replication stress that include slower replication fork speeds, evidence of stalled forks, and replication initiation from dormant replication origins. These findings have expanded on previous work demonstrating that extensive DNA damage in human PSC is replication associated. In this capacity, the DNA fiber assay has enabled the development of an advanced nucleoside-enriched culture medium that increases replication fork progression and decreases DNA damage and mitotic errors in human PSC cultures. The DNA fiber assay allows for the study of replication fork dynamics at single-molecule resolution. The assay relies on cells incorporating nucleotide analogs into nascent DNA during replication, which are then measured to monitor several replication parameters. Here we provide an optimized protocol for the fiber assay intended for use with human PSC, and describe the methods employed to analyze replication fork parameters. © 2020 Wiley Periodicals LLC. Basic Protocol 1: DNA fiber labeling Basic Protocol 2: DNA fiber spreading Basic Protocol 3: Immunostaining Support Protocol 1: Microscopy/data acquisition Support Protocol 2: Data analysis.
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Affiliation(s)
- Jason A Halliwell
- The Centre for Stem Cell Biology, University of Sheffield, Department of Biomedical Science, Sheffield, United Kingdom
| | - Polly Gravells
- Academic Unit of Molecular Oncology, Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
| | - Helen E Bryant
- Academic Unit of Molecular Oncology, Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
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Halliwell JA, Baker D, Judge K, Quail MA, Oliver K, Betteridge E, Skelton J, Andrews PW, Barbaric I. Nanopore Sequencing Indicates That Tandem Amplification of Chromosome 20q11.21 in Human Pluripotent Stem Cells Is Driven by Break-Induced Replication. Stem Cells Dev 2021; 30:578-586. [PMID: 33757297 PMCID: PMC8165465 DOI: 10.1089/scd.2021.0013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Copy number variants (CNVs) are genomic rearrangements implicated in numerous congenital and acquired diseases, including cancer. The appearance of culture-acquired CNVs in human pluripotent stem cells (PSCs) has prompted concerns for their use in regenerative medicine. A particular problem in PSC is the frequent occurrence of CNVs in the q11.21 region of chromosome 20. However, the exact mechanism of origin of this amplicon remains elusive due to the difficulty in delineating its sequence and breakpoints. Here, we have addressed this problem using long-read Nanopore sequencing of two examples of this CNV, present as duplication and as triplication. In both cases, the CNVs were arranged in a head-to-tail orientation, with microhomology sequences flanking or overlapping the proximal and distal breakpoints. These breakpoint signatures point to a mechanism of microhomology-mediated break-induced replication in CNV formation, with surrounding Alu sequences likely contributing to the instability of this genomic region.
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Affiliation(s)
- Jason A Halliwell
- Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - Duncan Baker
- Sheffield Diagnostic Genetic Services, Sheffield Children's Hospital, Sheffield, United Kingdom
| | - Kim Judge
- Department of Sequencing R & D, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Michael A Quail
- Department of Sequencing R & D, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Karen Oliver
- Department of Sequencing R & D, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Emma Betteridge
- Department of Sequencing R & D, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Jason Skelton
- Department of Sequencing R & D, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Peter W Andrews
- Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - Ivana Barbaric
- Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
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50
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Sustained intrinsic WNT and BMP4 activation impairs hESC differentiation to definitive endoderm and drives the cells towards extra-embryonic mesoderm. Sci Rep 2021; 11:8242. [PMID: 33859268 PMCID: PMC8050086 DOI: 10.1038/s41598-021-87547-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 03/31/2021] [Indexed: 12/13/2022] Open
Abstract
We identified a human embryonic stem cell subline that fails to respond to the differentiation cues needed to obtain endoderm derivatives, differentiating instead into extra-embryonic mesoderm. RNA-sequencing analysis showed that the subline has hyperactivation of the WNT and BMP4 signalling. Modulation of these pathways with small molecules confirmed them as the cause of the differentiation impairment. While activation of WNT and BMP4 in control cells resulted in a loss of endoderm differentiation and induction of extra-embryonic mesoderm markers, inhibition of these pathways in the subline restored its ability to differentiate. Karyotyping and exome sequencing analysis did not identify any changes in the genome that could account for the pathway deregulation. These findings add to the increasing evidence that different responses of stem cell lines to differentiation protocols are based on genetic and epigenetic factors, inherent to the line or acquired during cell culture.
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