1
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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 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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2
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Vales JP, Barbaric I. Culture-acquired genetic variation in human pluripotent stem cells: Twenty years on. Bioessays 2024:e2400062. [PMID: 38873900 DOI: 10.1002/bies.202400062] [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: 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 Biology, School of Biosciences, University of Sheffield, Sheffield, UK
- Neuroscience Institute, University of Sheffield, Sheffield, UK
- INSIGNEO Institute, University of Sheffield, Sheffield, UK
| | - Ivana Barbaric
- Centre for Stem Cell Biology, School of Biosciences, University of Sheffield, Sheffield, UK
- Neuroscience Institute, University of Sheffield, Sheffield, UK
- INSIGNEO Institute, University of Sheffield, Sheffield, UK
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3
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Yanagihara K, Hayashi Y, Liu Y, Yamaguchi T, Hemmi Y, Kokunugi M, Yamada KU, Fukumoto K, Suga M, Terada S, Nikawa H, Kawabata K, Furue M. Trisomy 12 compromises the mesendodermal differentiation propensity of human pluripotent stem cells. In Vitro Cell Dev Biol Anim 2024; 60:521-534. [PMID: 38169039 PMCID: PMC11126453 DOI: 10.1007/s11626-023-00824-9] [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: 08/12/2023] [Accepted: 09/08/2023] [Indexed: 01/05/2024]
Abstract
Trisomy 12 is one of the most frequent chromosomal abnormalities in cultured human pluripotent stem cells (hPSCs). Although potential oncogenic properties and augmented cell cycle caused by trisomy 12 have been reported, the consequences of trisomy 12 in terms of cell differentiation, which is the basis for regenerative medicine, drug development, and developmental biology studies, have not yet been investigated. Here, we report that trisomy 12 compromises the mesendodermal differentiation of hPSCs. We identified sublines of hPSCs carrying trisomy 12 after their prolonged culture. Transcriptome analysis revealed that these hPSC sublines carried abnormal gene expression patterns in specific signaling pathways in addition to cancer-related cell cycle pathways. These hPSC sublines showed a lower propensity for mesendodermal differentiation in embryoid bodies cultured in a serum-free medium. BMP4-induced exit from the self-renewal state was impaired in the trisomy 12 hPSC sublines, with less upregulation of key transcription factor gene expression. As a consequence, the differentiation efficiency of hematopoietic and hepatic lineages was also impaired in the trisomy 12 hPSC sublines. We reveal that trisomy 12 disrupts the genome-wide expression patterns that are required for proper mesendodermal differentiation.
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Affiliation(s)
- Kana Yanagihara
- Laboratory of Stem Cell Cultures, National Institutes of Biomedical Innovation, Health, and Nutrition, 7-6-8, Saito-Asagi, Osaka, Ibaraki, 567-0085, Japan
| | - Yohei Hayashi
- iPS Cell Advanced Characterization and Development Team, RIKEN Bioresource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan.
| | - Yujung Liu
- Laboratory of Stem Cell Cultures, National Institutes of Biomedical Innovation, Health, and Nutrition, 7-6-8, Saito-Asagi, Osaka, Ibaraki, 567-0085, Japan
| | - Tomoko Yamaguchi
- Laboratory of Cell Model for Drug Discovery, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8, Saito-Asagi, Osaka, Ibaraki, 567-0085, Japan
| | - Yasuko Hemmi
- iPS Cell Advanced Characterization and Development Team, RIKEN Bioresource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Minako Kokunugi
- Laboratory of Stem Cell Cultures, National Institutes of Biomedical Innovation, Health, and Nutrition, 7-6-8, Saito-Asagi, Osaka, Ibaraki, 567-0085, Japan
- Department of Oral Biology & Engineering Integrated Health Sciences, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kozue Uchio Yamada
- Laboratory of Animal Models for Human Diseases, National Institutes of Biomedical Innovation, Health, and Nutrition, 7-6-8, Saito-Asagi, Osaka, Ibaraki, 567-0085, Japan
| | - Ken Fukumoto
- Laboratory of Stem Cell Cultures, National Institutes of Biomedical Innovation, Health, and Nutrition, 7-6-8, Saito-Asagi, Osaka, Ibaraki, 567-0085, Japan
- Department of Applied Chemistry and Biotechnology, University of Fukui, Fukui City, 3-9-1 Bunkyo, Fukui, 910-8507, Japan
| | - Mika Suga
- Laboratory of Stem Cell Cultures, National Institutes of Biomedical Innovation, Health, and Nutrition, 7-6-8, Saito-Asagi, Osaka, Ibaraki, 567-0085, Japan
| | - Satoshi Terada
- Department of Applied Chemistry and Biotechnology, University of Fukui, Fukui City, 3-9-1 Bunkyo, Fukui, 910-8507, Japan
| | - Hiroki Nikawa
- Department of Oral Biology & Engineering Integrated Health Sciences, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kenji Kawabata
- Laboratory of Cell Model for Drug Discovery, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8, Saito-Asagi, Osaka, Ibaraki, 567-0085, Japan
| | - Miho Furue
- Laboratory of Stem Cell Cultures, National Institutes of Biomedical Innovation, Health, and Nutrition, 7-6-8, Saito-Asagi, Osaka, Ibaraki, 567-0085, Japan.
- Cel-MiM, Ltd., Tokyo, Japan.
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Hosea R, Hillary S, Naqvi S, Wu S, Kasim V. The two sides of chromosomal instability: drivers and brakes in cancer. Signal Transduct Target Ther 2024; 9:75. [PMID: 38553459 PMCID: PMC10980778 DOI: 10.1038/s41392-024-01767-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/18/2024] [Accepted: 02/06/2024] [Indexed: 04/02/2024] Open
Abstract
Chromosomal instability (CIN) is a hallmark of cancer and is associated with tumor cell malignancy. CIN triggers a chain reaction in cells leading to chromosomal abnormalities, including deviations from the normal chromosome number or structural changes in chromosomes. CIN arises from errors in DNA replication and chromosome segregation during cell division, leading to the formation of cells with abnormal number and/or structure of chromosomes. Errors in DNA replication result from abnormal replication licensing as well as replication stress, such as double-strand breaks and stalled replication forks; meanwhile, errors in chromosome segregation stem from defects in chromosome segregation machinery, including centrosome amplification, erroneous microtubule-kinetochore attachments, spindle assembly checkpoint, or defective sister chromatids cohesion. In normal cells, CIN is deleterious and is associated with DNA damage, proteotoxic stress, metabolic alteration, cell cycle arrest, and senescence. Paradoxically, despite these negative consequences, CIN is one of the hallmarks of cancer found in over 90% of solid tumors and in blood cancers. Furthermore, CIN could endow tumors with enhanced adaptation capabilities due to increased intratumor heterogeneity, thereby facilitating adaptive resistance to therapies; however, excessive CIN could induce tumor cells death, leading to the "just-right" model for CIN in tumors. Elucidating the complex nature of CIN is crucial for understanding the dynamics of tumorigenesis and for developing effective anti-tumor treatments. This review provides an overview of causes and consequences of CIN, as well as the paradox of CIN, a phenomenon that continues to perplex researchers. Finally, this review explores the potential of CIN-based anti-tumor therapy.
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Affiliation(s)
- Rendy Hosea
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Sharon Hillary
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Sumera Naqvi
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Shourong Wu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China.
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing University, Chongqing, 400030, China.
| | - Vivi Kasim
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China.
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing University, Chongqing, 400030, China.
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5
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Natesan G, Hamilton T, Deeds EJ, Shah PK. Novel metrics reveal new structure and unappreciated heterogeneity in Caenorhabditis elegans development. PLoS Comput Biol 2023; 19:e1011733. [PMID: 38113280 PMCID: PMC10763962 DOI: 10.1371/journal.pcbi.1011733] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 01/03/2024] [Accepted: 12/04/2023] [Indexed: 12/21/2023] Open
Abstract
High throughput experimental approaches are increasingly allowing for the quantitative description of cellular and organismal phenotypes. Distilling these large volumes of complex data into meaningful measures that can drive biological insight remains a central challenge. In the quantitative study of development, for instance, one can resolve phenotypic measures for single cells onto their lineage history, enabling joint consideration of heritable signals and cell fate decisions. Most attempts to analyze this type of data, however, discard much of the information content contained within lineage trees. In this work we introduce a generalized metric, which we term the branch edit distance, that allows us to compare any two embryos based on phenotypic measurements in individual cells. This approach aligns those phenotypic measurements to the underlying lineage tree, providing a flexible and intuitive framework for quantitative comparisons between, for instance, Wild-Type (WT) and mutant developmental programs. We apply this novel metric to data on cell-cycle timing from over 1300 WT and RNAi-treated Caenorhabditis elegans embryos. Our new metric revealed surprising heterogeneity within this data set, including subtle batch effects in WT embryos and dramatic variability in RNAi-induced developmental phenotypes, all of which had been missed in previous analyses. Further investigation of these results suggests a novel, quantitative link between pathways that govern cell fate decisions and pathways that pattern cell cycle timing in the early embryo. Our work demonstrates that the branch edit distance we propose, and similar metrics like it, have the potential to revolutionize our quantitative understanding of organismal phenotype.
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Affiliation(s)
- Gunalan Natesan
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United States of America
| | - Timothy Hamilton
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California, United States of America
| | - Eric J. Deeds
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California, United States of America
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, California, United States of America
| | - Pavak K. Shah
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United States of America
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, California, United States of America
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6
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Domingo-Reinés J, Montes R, Garcia-Moreno A, Gallardo A, Sanchez-Manas JM, Ellson I, Lamolda M, Calabro C, López-Escamez JA, Catalina P, Carmona-Sáez P, Real PJ, Landeira D, Ramos-Mejia V. The pediatric leukemia oncoprotein NUP98-KDM5A induces genomic instability that may facilitate malignant transformation. Cell Death Dis 2023; 14:357. [PMID: 37301844 PMCID: PMC10257648 DOI: 10.1038/s41419-023-05870-5] [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: 07/12/2022] [Revised: 04/28/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023]
Abstract
Pediatric Acute Myeloid Leukemia (AML) is a rare and heterogeneous disease characterized by a high prevalence of gene fusions as driver mutations. Despite the improvement of survival in the last years, about 50% of patients still experience a relapse. It is not possible to improve prognosis only with further intensification of chemotherapy, as come with a severe cost to the health of patients, often resulting in treatment-related death or long-term sequels. To design more effective and less toxic therapies we need a better understanding of pediatric AML biology. The NUP98-KDM5A chimeric protein is exclusively found in a particular subgroup of young pediatric AML patients with complex karyotypes and poor prognosis. In this study, we investigated the impact of NUP98-KDM5A expression on cellular processes in human Pluripotent Stem Cell models and a patient-derived cell line. We found that NUP98-KDM5A generates genomic instability through two complementary mechanisms that involve accumulation of DNA damage and direct interference of RAE1 activity during mitosis. Overall, our data support that NUP98-KDM5A promotes genomic instability and likely contributes to malignant transformation.
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Grants
- Asociación de Madres y Padres de Niños Oncológicos de Granada (AUPA), Asociación El Mundo de Namu, and the Ministry of Science and Innovation, FECYT-Precipita: SURUS, Cristina Molinos, Salvador Rigol
- Universidad de Granada (University of Granada)
- Andalusian Regional Ministry of Economic Transformation, Industry, Knowledge and Universities (PREDOC_01765) grant.
- Consejería de Salud, Junta de Andalucía (Ministry of Health, Andalusian Regional Government)
- Spanish Ministry for Science and Innovation (PID2020-119032RB-I00) and FEDER/Junta de Andalucía- Consejería de Transformación Económica, Industria, Conocimiento y Universidades (P20_00335)
- Ministerio de Economía y Competitividad (Ministry of Economy and Competitiveness)
- Spanish Ministry for Science and Innovation (EUR2021-122005; PID2019-108108-100), the Andalusian Regional Government (PC-0246-2017; PY20_00681)
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Affiliation(s)
- Joan Domingo-Reinés
- GENYO, Centre for Genomics and Oncological Research Pfizer - University of Granada - Andalusian Regional Government, PTS, 18016, Granada, Spain
| | - Rosa Montes
- GENYO, Centre for Genomics and Oncological Research Pfizer - University of Granada - Andalusian Regional Government, PTS, 18016, Granada, Spain
- Department of Cell Biology, Faculty of Sciences, University of Granada, 18071, Granada, Spain
| | - Adrián Garcia-Moreno
- GENYO, Centre for Genomics and Oncological Research Pfizer - University of Granada - Andalusian Regional Government, PTS, 18016, Granada, Spain
| | - Amador Gallardo
- GENYO, Centre for Genomics and Oncological Research Pfizer - University of Granada - Andalusian Regional Government, PTS, 18016, Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, 18071, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| | - Jose Manuel Sanchez-Manas
- GENYO, Centre for Genomics and Oncological Research Pfizer - University of Granada - Andalusian Regional Government, PTS, 18016, Granada, Spain
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, 18071, Granada, Spain
| | - Iván Ellson
- GENYO, Centre for Genomics and Oncological Research Pfizer - University of Granada - Andalusian Regional Government, PTS, 18016, Granada, Spain
| | - Mar Lamolda
- GENYO, Centre for Genomics and Oncological Research Pfizer - University of Granada - Andalusian Regional Government, PTS, 18016, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
| | - Chiara Calabro
- GENYO, Centre for Genomics and Oncological Research Pfizer - University of Granada - Andalusian Regional Government, PTS, 18016, Granada, Spain
| | - Jose Antonio López-Escamez
- GENYO, Centre for Genomics and Oncological Research Pfizer - University of Granada - Andalusian Regional Government, PTS, 18016, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
- Meniere's Disease Neuroscience Research Program, Faculty of Medicine & Health, School of Medical Sciences, The Kolling Institute, University of Sydney, Sydney, NSW, Australia
| | - Purificación Catalina
- Andalusian Public Health System Biobank, Coordinating Node, Av. del Conocimiento, S/N, 18016, Granada, Spain
| | - Pedro Carmona-Sáez
- GENYO, Centre for Genomics and Oncological Research Pfizer - University of Granada - Andalusian Regional Government, PTS, 18016, Granada, Spain
- Department of Statistics, University of Granada, 18071, Granada, Spain
- Excellence Research Unit "Modeling Nature" (MNat), University of Granada, 18016, Granada, Spain
| | - Pedro J Real
- GENYO, Centre for Genomics and Oncological Research Pfizer - University of Granada - Andalusian Regional Government, PTS, 18016, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, 18071, Granada, Spain
| | - David Landeira
- GENYO, Centre for Genomics and Oncological Research Pfizer - University of Granada - Andalusian Regional Government, PTS, 18016, Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, 18071, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| | - Verónica Ramos-Mejia
- GENYO, Centre for Genomics and Oncological Research Pfizer - University of Granada - Andalusian Regional Government, PTS, 18016, Granada, Spain.
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7
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Natesan G, Hamilton T, Deeds EJ, Shah PK. Novel metrics reveal new structure and unappreciated heterogeneity in C. elegans development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.12.540617. [PMID: 37292606 PMCID: PMC10245744 DOI: 10.1101/2023.05.12.540617] [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
High throughput experimental approaches are increasingly allowing for the quantitative description of cellular and organismal phenotypes. Distilling these large volumes of complex data into meaningful measures that can drive biological insight remains a central challenge. In the quantitative study of development, for instance, one can resolve phenotypic measures for single cells onto their lineage history, enabling joint consideration of heritable signals and cell fate decisions. Most attempts to analyze this type of data, however, discard much of the information content contained within lineage trees. In this work we introduce a generalized metric, which we term the branch distance, that allows us to compare any two embryos based on phenotypic measurements in individual cells. This approach aligns those phenotypic measurements to the underlying lineage tree, providing a flexible and intuitive framework for quantitative comparisons between, for instance, Wild-Type (WT) and mutant developmental programs. We apply this novel metric to data on cell-cycle timing from over 1300 WT and RNAi-treated Caenorhabditis elegans embryos. Our new metric revealed surprising heterogeneity within this data set, including subtle batch effects in WT embryos and dramatic variability in RNAi-induced developmental phenotypes, all of which had been missed in previous analyses. Further investigation of these results suggests a novel, quantitative link between pathways that govern cell fate decisions and pathways that pattern cell cycle timing in the early embryo. Our work demonstrates that the branch distance we propose, and similar metrics like it, have the potential to revolutionize our quantitative understanding of organismal phenotype.
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Affiliation(s)
- Gunalan Natesan
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA
| | - Timothy Hamilton
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA
| | - Eric J. Deeds
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA
| | - Pavak K. Shah
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA
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8
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Cohen PJR, Luquet E, Pletenka J, Leonard A, Warter E, Gurchenkov B, Carrere J, Rieu C, Hardouin J, Moncaubeig F, Lanero M, Quelennec E, Wurtz H, Jamet E, Demarco M, Banal C, Van Liedekerke P, Nassoy P, Feyeux M, Lefort N, Alessandri K. Engineering 3D micro-compartments for highly efficient and scale-independent expansion of human pluripotent stem cells in bioreactors. Biomaterials 2023; 295:122033. [PMID: 36764194 DOI: 10.1016/j.biomaterials.2023.122033] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 12/12/2022] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
Human pluripotent stem cells (hPSCs) have emerged as the most promising cellular source for cell therapies. To overcome the scale-up limitations of classical 2D culture systems, suspension cultures have been developed to meet the need for large-scale culture in regenerative medicine. Despite constant improvements, current protocols that use microcarriers or generate cell aggregates only achieve moderate amplification performance. Here, guided by reports showing that hPSCs can self-organize in vitro into cysts reminiscent of the epiblast stage in embryo development, we developed a physio-mimetic approach for hPSC culture. We engineered stem cell niche microenvironments inside microfluidics-assisted core-shell microcapsules. We demonstrate that lumenized three-dimensional colonies significantly improve viability and expansion rates while maintaining pluripotency compared to standard hPSC culture platforms such as 2D cultures, microcarriers, and aggregates. By further tuning capsule size and culture conditions, we scale up this method to industrial-scale stirred tank bioreactors and achieve an unprecedented hPSC amplification rate of 277-fold in 6.5 days. In brief, our findings indicate that our 3D culture system offers a suitable strategy both for basic stem cell biology experiments and for clinical applications.
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Affiliation(s)
- Philippe J R Cohen
- Université Paris Cité, Imagine Institute, IPSC Core Facility, INSERM UMR U1163, F-75015, Paris, France; Treefrog Therapeutics, F-33600, Pessac, France.
| | | | | | | | | | | | | | | | | | | | | | - Eddy Quelennec
- Université Paris Cité, Imagine Institute, IPSC Core Facility, INSERM UMR U1163, F-75015, Paris, France; Treefrog Therapeutics, F-33600, Pessac, France
| | | | | | | | - Celine Banal
- Université Paris Cité, Imagine Institute, IPSC Core Facility, INSERM UMR U1163, F-75015, Paris, France
| | - Paul Van Liedekerke
- Inria Paris & Sorbonne Université LJLL, 2 Rue Simone IFF, F-75012, Paris, France
| | - Pierre Nassoy
- LP2N, Laboratoire Photonique Numérique et Nanosciences, Univ. Bordeaux, F-33400, Talence, France; Institut D'Optique Graduate School & CNRS UMR 5298, F-33400, Talence, France
| | | | - Nathalie Lefort
- Université Paris Cité, Imagine Institute, IPSC Core Facility, INSERM UMR U1163, F-75015, Paris, France
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9
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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: 2.0] [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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10
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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: 5] [Impact Index Per Article: 5.0] [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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11
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Tristan CA, Hong H, Jethmalani Y, Chen Y, Weber C, Chu PH, Ryu S, Jovanovic VM, Hur I, Voss TC, Simeonov A, Singeç I. Efficient and safe single-cell cloning of human pluripotent stem cells using the CEPT cocktail. Nat Protoc 2023; 18:58-80. [PMID: 36261632 PMCID: PMC11009857 DOI: 10.1038/s41596-022-00753-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 07/05/2022] [Indexed: 01/14/2023]
Abstract
Human pluripotent stem cells (hPSCs) are inherently sensitive cells. Single-cell dissociation and the establishment of clonal cell lines have been long-standing challenges. This inefficiency of cell cloning represents a major obstacle for the standardization and streamlining of gene editing in induced pluripotent stem cells for basic and translational research. Here we describe a chemically defined protocol for robust single-cell cloning using microfluidics-based cell sorting in combination with the CEPT small-molecule cocktail. This advanced strategy promotes the viability and cell fitness of self-renewing stem cells. The use of low-pressure microfluidic cell dispensing ensures gentle and rapid dispensing of single cells into 96- and 384-well plates, while the fast-acting CEPT cocktail minimizes cellular stress and maintains cell structure and function immediately after cell dissociation. The protocol also facilitates clone picking and produces genetically stable clonal cell lines from hPSCs in a safe and cost-efficient fashion. Depending on the proliferation rate of the clone derived from a single cell, this protocol can be completed in 7-14 d and requires experience with aseptic cell culture techniques. Altogether, the relative ease, scalability and robustness of this workflow should boost gene editing in hPSCs and leverage a wide range of applications, including cell line development (e.g., reporter and isogenic cell lines), disease modeling and applications in regenerative medicine.
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Affiliation(s)
- Carlos A Tristan
- Stem Cell Translation Laboratory (SCTL), Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, USA.
| | - Hyenjong Hong
- Stem Cell Translation Laboratory (SCTL), Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, USA
| | - Yogita Jethmalani
- Stem Cell Translation Laboratory (SCTL), Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, USA
| | - Yu Chen
- Stem Cell Translation Laboratory (SCTL), Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, USA
| | - Claire Weber
- Stem Cell Translation Laboratory (SCTL), Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, USA
| | - Pei-Hsuan Chu
- Stem Cell Translation Laboratory (SCTL), Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, USA
| | - Seungmi Ryu
- Stem Cell Translation Laboratory (SCTL), Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, USA
| | - Vukasin M Jovanovic
- Stem Cell Translation Laboratory (SCTL), Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, USA
| | - Inae Hur
- Stem Cell Translation Laboratory (SCTL), Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, USA
| | - Ty C Voss
- Stem Cell Translation Laboratory (SCTL), Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, USA
| | - Anton Simeonov
- Stem Cell Translation Laboratory (SCTL), Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, USA
| | - Ilyas Singeç
- Stem Cell Translation Laboratory (SCTL), Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, USA.
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12
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Mamaeva A, Krasnova O, Khvorova I, Kozlov K, Gursky V, Samsonova M, Tikhonova O, Neganova I. Quality Control of Human Pluripotent Stem Cell Colonies by Computational Image Analysis Using Convolutional Neural Networks. Int J Mol Sci 2022; 24:ijms24010140. [PMID: 36613583 PMCID: PMC9820636 DOI: 10.3390/ijms24010140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/08/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
Human pluripotent stem cells are promising for a wide range of research and therapeutic purposes. Their maintenance in culture requires the deep control of their pluripotent and clonal status. A non-invasive method for such control involves day-to-day observation of the morphological changes, along with imaging colonies, with the subsequent automatic assessment of colony phenotype using image analysis by machine learning methods. We developed a classifier using a convolutional neural network and applied it to discriminate between images of human embryonic stem cell (hESC) colonies with "good" and "bad" morphological phenotypes associated with a high and low potential for pluripotency and clonality maintenance, respectively. The training dataset included the phase-contrast images of hESC line H9, in which the morphological phenotype of each colony was assessed through visual analysis. The classifier showed a high level of accuracy (89%) in phenotype prediction. By training the classifier on cropped images of various sizes, we showed that the spatial scale of ~144 μm was the most informative in terms of classification quality, which was an intermediate size between the characteristic diameters of a single cell (~15 μm) and the entire colony (~540 μm). We additionally performed a proteomic analysis of several H9 cell samples used in the computational analysis and showed that cells of different phenotypes differentiated at the molecular level. Our results indicated that the proposed approach could be used as an effective method of non-invasive automated analysis to identify undesirable developmental anomalies during the propagation of pluripotent stem cells.
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Affiliation(s)
- Anastasiya Mamaeva
- Mathematical Biology and Bioinformatics Lab, Peter the Great St. Petersburg Polytechnic University, 195251 Saint Petersburg, Russia
| | - Olga Krasnova
- Institute of Cytology, 194064 Saint Petersburg, Russia
| | - Irina Khvorova
- Faculty of Biology, Saint-Petersburg State University, 199034 Saint Petersburg, Russia
| | - Konstantin Kozlov
- Mathematical Biology and Bioinformatics Lab, Peter the Great St. Petersburg Polytechnic University, 195251 Saint Petersburg, Russia
| | | | - Maria Samsonova
- Mathematical Biology and Bioinformatics Lab, Peter the Great St. Petersburg Polytechnic University, 195251 Saint Petersburg, Russia
| | - Olga Tikhonova
- Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Irina Neganova
- Institute of Cytology, 194064 Saint Petersburg, Russia
- Correspondence:
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13
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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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14
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Krasnova OA, Gursky VV, Chabina AS, Kulakova KA, Alekseenko LL, Panova AV, Kiselev SL, Neganova IE. Prognostic Analysis of Human Pluripotent Stem Cells Based on Their Morphological Portrait and Expression of Pluripotent Markers. Int J Mol Sci 2022; 23:12902. [PMID: 36361693 PMCID: PMC9656397 DOI: 10.3390/ijms232112902] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 11/26/2023] Open
Abstract
The ability of human pluripotent stem cells for unlimited proliferation and self-renewal promotes their application in the fields of regenerative medicine. The morphological assessment of growing colonies and cells, as a non-invasive method, allows the best clones for further clinical applications to be safely selected. For this purpose, we analyzed seven morphological parameters of both colonies and cells extracted from the phase-contrast images of human embryonic stem cell line H9, control human induced pluripotent stem cell (hiPSC) line AD3, and hiPSC line HPCASRi002-A (CaSR) in various passages during their growth for 120 h. The morphological phenotype of each colony was classified using a visual analysis and associated with its potential for pluripotency and clonality maintenance, thus defining the colony phenotype as the control parameter. Using the analysis of variance for the morphological parameters of each line, we showed that selected parameters carried information about different cell lines and different phenotypes within each line. We demonstrated that a model of classification of colonies and cells by phenotype, built on the selected parameters as predictors, recognized the phenotype with an accuracy of 70-75%. In addition, we performed a qRT-PCR analysis of eleven pluripotency markers genes. By analyzing the variance of their expression in samples from different lines and with different phenotypes, we identified group-specific sets of genes that could be used as the most informative ones for the separation of the best clones. Our results indicated the fundamental possibility of constructing a morphological portrait of a colony informative for the automatic identification of the phenotype and for linking this portrait to the expression of pluripotency markers.
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Affiliation(s)
| | - Vitaly V. Gursky
- Institute of Cytology, 194064 Saint Petersburg, Russia
- Ioffe Institute, 194021 Saint Petersburg, Russia
| | | | | | | | - Alexandra V. Panova
- Endocrinology Research Centre, 115478 Moscow, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 117971 Moscow, Russia
| | - Sergey L. Kiselev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 117971 Moscow, Russia
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15
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Tristan CA, Ormanoglu P, Slamecka J, Malley C, Chu PH, Jovanovic VM, Gedik Y, Jethmalani Y, Bonney C, Barnaeva E, Braisted J, Mallanna SK, Dorjsuren D, Iannotti MJ, Voss TC, Michael S, Simeonov A, Singeç I. Robotic high-throughput biomanufacturing and functional differentiation of human pluripotent stem cells. Stem Cell Reports 2021; 16:3076-3092. [PMID: 34861164 PMCID: PMC8693769 DOI: 10.1016/j.stemcr.2021.11.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/02/2021] [Accepted: 11/04/2021] [Indexed: 12/21/2022] Open
Abstract
Efficient translation of human induced pluripotent stem cells (hiPSCs) requires scalable cell manufacturing strategies for optimal self-renewal and functional differentiation. Traditional manual cell culture is variable and labor intensive, posing challenges for high-throughput applications. Here, we established a robotic platform and automated all essential steps of hiPSC culture and differentiation under chemically defined conditions. This approach allowed rapid and standardized manufacturing of billions of hiPSCs that can be produced in parallel from up to 90 different patient- and disease-specific cell lines. Moreover, we established automated multi-lineage differentiation and generated functional neurons, cardiomyocytes, and hepatocytes. To validate our approach, we compared robotic and manual cell culture operations and performed comprehensive molecular and cellular characterizations (e.g., single-cell transcriptomics, mass cytometry, metabolism, electrophysiology) to benchmark industrial-scale cell culture operations toward building an integrated platform for efficient cell manufacturing for disease modeling, drug screening, and cell therapy.
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Affiliation(s)
- Carlos A Tristan
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation (DPI), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Pinar Ormanoglu
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation (DPI), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Jaroslav Slamecka
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation (DPI), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Claire Malley
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation (DPI), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Pei-Hsuan Chu
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation (DPI), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Vukasin M Jovanovic
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation (DPI), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Yeliz Gedik
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation (DPI), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Yogita Jethmalani
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation (DPI), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Charles Bonney
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation (DPI), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Elena Barnaeva
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation (DPI), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - John Braisted
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation (DPI), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Sunil K Mallanna
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation (DPI), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Dorjbal Dorjsuren
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation (DPI), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Michael J Iannotti
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation (DPI), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Ty C Voss
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation (DPI), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Sam Michael
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation (DPI), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation (DPI), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Ilyas Singeç
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation (DPI), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), 9800 Medical Center Drive, Rockville, MD 20850, USA.
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16
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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: 33] [Impact Index Per Article: 11.0] [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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17
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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: 1.0] [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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18
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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: 0.7] [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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19
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Armstrong JPK, Keane TJ, Roques AC, Patrick PS, Mooney CM, Kuan WL, Pisupati V, Oreffo ROC, Stuckey DJ, Watt FM, Forbes SJ, Barker RA, Stevens MM. A blueprint for translational regenerative medicine. Sci Transl Med 2021; 12:12/572/eaaz2253. [PMID: 33268507 DOI: 10.1126/scitranslmed.aaz2253] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 03/05/2020] [Indexed: 12/11/2022]
Abstract
The past few decades have produced a large number of proof-of-concept studies in regenerative medicine. However, the route to clinical adoption is fraught with technical and translational obstacles that frequently consign promising academic solutions to the so-called "valley of death." Here, we present a proposed blueprint for translational regenerative medicine. We offer principles to help guide the selection of cells and materials, present key in vivo imaging modalities, and argue that the host immune response should be considered throughout design and development. Last, we suggest a pathway to navigate the often complex regulatory and manufacturing landscape of translational regenerative medicine.
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Affiliation(s)
- James P K Armstrong
- Department of Materials, Imperial College London, London SW7 2AZ, UK. .,Department of Bioengineering, Imperial College London, London SW7 2AZ, UK.,Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Timothy J Keane
- Department of Materials, Imperial College London, London SW7 2AZ, UK.,Department of Bioengineering, Imperial College London, London SW7 2AZ, UK.,Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Anne C Roques
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
| | - P Stephen Patrick
- Centre for Advanced Biomedical Imaging, University College London, London WC1E 6DD, UK
| | - Claire M Mooney
- Centre for Stem Cells and Regenerative Medicine, King's College London, London SE1 9RT, UK
| | - Wei-Li Kuan
- John van Geest Centre for Brain Repair and Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0PY, UK
| | - Venkat Pisupati
- John van Geest Centre for Brain Repair and Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0PY, UK
| | - Richard O C Oreffo
- Centre for Human Development, Stem Cells and Regeneration, University of Southampton, Southampton SO16 6YD, UK
| | - Daniel J Stuckey
- Centre for Advanced Biomedical Imaging, University College London, London WC1E 6DD, UK
| | - Fiona M Watt
- Centre for Stem Cells and Regenerative Medicine, King's College London, London SE1 9RT, UK
| | - Stuart J Forbes
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Roger A Barker
- John van Geest Centre for Brain Repair and Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0PY, UK
| | - Molly M Stevens
- Department of Materials, Imperial College London, London SW7 2AZ, UK. .,Department of Bioengineering, Imperial College London, London SW7 2AZ, UK.,Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, UK
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20
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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: 1.3] [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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21
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Lin SC, Loza A, Antrim L, Talbot P. Video bioinformatics analysis of human pluripotent stem cell morphology, quality, and cellular dynamics. Stem Cells Transl Med 2021; 10:1343-1359. [PMID: 34089307 PMCID: PMC8380446 DOI: 10.1002/sctm.15-0352] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 04/04/2021] [Accepted: 04/20/2021] [Indexed: 12/31/2022] Open
Abstract
StemCellQC is a video bioinformatics software tool for the quantitative analysis of human pluripotent stem cell (hPSC) colonies. Our objective was to use StemCellQC to evaluate and compare various experimental culture conditions, cell lines, and treatments and to demonstrate its applicability to PSC problems. Seven key features were identified that provided useful information on PSC morphology, dynamic behavior, and viability. Colony attachment was better on laminin‐521 than on Matrigel and Geltrex. Growth rates were similar on each matrix when data were normalized. The brightness/area ratio feature showed greater cell death in colonies grown on Matrigel and Geltrex than on laminin‐521 further contributing to an overall greater yield of cells on laminin‐521. Four different PSC culture media performed similarly; however, one medium produced batch‐to‐batch variation in colony morphology and dynamic features. Two embryonic and one induced pluripotent stem cell line showed significant differences in morphology, growth rates, motility, and death rates. Cells from the same vial that became phenotypically different in culture showed measurable differences in morphology, brightness, and motility. Likewise, differentiating and undifferentiated colonies varied in growth rate, intensity, and motility. Three pluripotent cell lines treated with a low concentration of cinnamaldehyde, a chemical used in consumer products, showed adverse effects and differed in their sensitivity to treatment. Our data demonstrate various applications of StemCellQC which could be used in basic and translational research, toxicological and drug testing, and clinical facilities engaged in stem cell therapy.
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Affiliation(s)
- Sabrina C Lin
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California, USA
| | - Antonio Loza
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California, USA
| | - Lauren Antrim
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California, USA
| | - Prue Talbot
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California, USA
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22
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Zaaijer S, Groen SC, Sanjana NE. Tracking cell lineages to improve research reproducibility. Nat Biotechnol 2021; 39:666-670. [PMID: 34012093 PMCID: PMC9644290 DOI: 10.1038/s41587-021-00928-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Sophie Zaaijer
- Cornell Tech, New York, NY, USA,FIND Genomics, New York, NY, USA
| | - Simon C. Groen
- Department of Biology, New York University, New York, NY, USA
| | - Neville E. Sanjana
- Department of Biology, New York University, New York, NY, USA,New York Genome Center, New York, NY, USA
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23
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Chen Y, Tristan CA, Chen L, Jovanovic VM, Malley C, Chu PH, Ryu S, Deng T, Ormanoglu P, Tao D, Fang Y, Slamecka J, Hong H, LeClair CA, Michael S, Austin CP, Simeonov A, Singeç I. A versatile polypharmacology platform promotes cytoprotection and viability of human pluripotent and differentiated cells. Nat Methods 2021; 18:528-541. [PMID: 33941937 PMCID: PMC8314867 DOI: 10.1038/s41592-021-01126-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 03/22/2021] [Indexed: 12/27/2022]
Abstract
Clinical translation of human pluripotent stem cells (hPSCs) requires advanced strategies that ensure safe and robust long-term growth and functional differentiation. Pluripotent cells are capable of extensive self-renewal, yet remain highly sensitive to environmental perturbations in vitro, posing challenges to their therapeutic use. Here, we deployed innovative high-throughput screening strategies to identify a small molecule cocktail that dramatically improves viability of hPSCs and their differentiated progeny. The combination of Chroman 1, Emricasan, Polyamines, and Trans-ISRIB (CEPT) enhanced cell survival of genetically stable hPSCs by simultaneously blocking several stress mechanisms that otherwise compromise cell structure and function. CEPT provided strong improvements for several key applications in stem cell research, including routine cell passaging, cryopreservation of pluripotent and differentiated cells, embryoid body (EB) and organoid formation, single-cell cloning, and genome editing. Thus, CEPT represents a unique polypharmacology strategy for comprehensive cytoprotection, providing a new rationale for efficient and safe utilization of hPSCs. Conferring cell fitness by multi-target drug combinations may become a common approach in cryobiology, drug development, and regenerative medicine.
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Affiliation(s)
- Yu Chen
- National Center for Advancing Translational Sciences (NCATS), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD, USA
| | - Carlos A Tristan
- National Center for Advancing Translational Sciences (NCATS), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD, USA
| | - Lu Chen
- National Center for Advancing Translational Sciences (NCATS), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD, USA
| | - Vukasin M Jovanovic
- National Center for Advancing Translational Sciences (NCATS), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD, USA
| | - Claire Malley
- National Center for Advancing Translational Sciences (NCATS), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD, USA
| | - Pei-Hsuan Chu
- National Center for Advancing Translational Sciences (NCATS), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD, USA
| | - Seungmi Ryu
- National Center for Advancing Translational Sciences (NCATS), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD, USA
| | - Tao Deng
- National Center for Advancing Translational Sciences (NCATS), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD, USA
| | - Pinar Ormanoglu
- National Center for Advancing Translational Sciences (NCATS), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD, USA
| | - Dingyin Tao
- National Center for Advancing Translational Sciences (NCATS), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD, USA
| | - Yuhong Fang
- National Center for Advancing Translational Sciences (NCATS), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD, USA
| | - Jaroslav Slamecka
- National Center for Advancing Translational Sciences (NCATS), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD, USA
| | - Hyenjong Hong
- National Center for Advancing Translational Sciences (NCATS), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD, USA
| | - Christopher A LeClair
- National Center for Advancing Translational Sciences (NCATS), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD, USA
| | - Sam Michael
- National Center for Advancing Translational Sciences (NCATS), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD, USA
| | - Christopher P Austin
- National Center for Advancing Translational Sciences (NCATS), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences (NCATS), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD, USA
| | - Ilyas Singeç
- National Center for Advancing Translational Sciences (NCATS), Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD, USA.
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24
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Hirose T, Kotoku J, Toki F, Nishimura EK, Nanba D. Label-free quality control and identification of human keratinocyte stem cells by deep learning-based automated cell tracking. Stem Cells 2021; 39:1091-1100. [PMID: 33783921 PMCID: PMC8359832 DOI: 10.1002/stem.3371] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/23/2021] [Indexed: 01/07/2023]
Abstract
Stem cell-based products have clinical and industrial applications. Thus, there is a need to develop quality control methods to standardize stem cell manufacturing. Here, we report a deep learning-based automated cell tracking (DeepACT) technology for noninvasive quality control and identification of cultured human stem cells. The combination of deep learning-based cascading cell detection and Kalman filter algorithm-based tracking successfully tracked the individual cells within the densely packed human epidermal keratinocyte colonies in the phase-contrast images of the culture. DeepACT rapidly analyzed the motion of individual keratinocytes, which enabled the quantitative evaluation of keratinocyte dynamics in response to changes in culture conditions. Furthermore, DeepACT can distinguish keratinocyte stem cell colonies from non-stem cell-derived colonies by analyzing the spatial and velocity information of cells. This system can be widely applied to stem cell cultures used in regenerative medicine and provides a platform for developing reliable and noninvasive quality control technology.
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Affiliation(s)
- Takuya Hirose
- Graduate School of Medical Care and Technology, Teikyo University, Tokyo, Japan
| | - Jun'ichi Kotoku
- Graduate School of Medical Care and Technology, Teikyo University, Tokyo, Japan
| | - Fujio Toki
- Department of Stem Cell Biology, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Emi K Nishimura
- Department of Stem Cell Biology, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.,Division of Aging and Regeneration, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Daisuke Nanba
- Department of Stem Cell Biology, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
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25
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Abstract
Acquired chromosomal abnormalities may occur during the reprogramming and culture of human pluripotent stem cells (hPSCs). Therefore, it is required that regular testing of genetic integrity be conducted. G-banded karyotyping is a widely used genetic assay that is capable of detecting chromosomal abnormalities. Karyotyping of hPSC cultures can be a challenging undertaking for inexperienced investigators; here, we provide detailed procedures for karyotyping, including sample preparation and analysis, as well as the interpretation of hPSC karyotype results.
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26
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Halliwell J, Barbaric I, Andrews PW. Acquired genetic changes in human pluripotent stem cells: origins and consequences. Nat Rev Mol Cell Biol 2020; 21:715-728. [DOI: 10.1038/s41580-020-00292-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2020] [Indexed: 12/14/2022]
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27
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Tristan CA, Ormanoglu P, Slamecka J, Malley C, Chu PH, Jovanovic VM, Gedik Y, Bonney C, Barnaeva E, Braisted J, Mallanna SK, Dorjsuren D, Iannotti MJ, Voss TC, Michael S, Simeonov A, Singeç I. Robotic High-Throughput Biomanufacturing and Functional Differentiation of Human Pluripotent Stem Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.08.03.235242. [PMID: 32793899 PMCID: PMC7418713 DOI: 10.1101/2020.08.03.235242] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Efficient translation of human induced pluripotent stem cells (hiPSCs) depends on implementing scalable cell manufacturing strategies that ensure optimal self-renewal and functional differentiation. Currently, manual culture of hiPSCs is highly variable and labor-intensive posing significant challenges for high-throughput applications. Here, we established a robotic platform and automated all essential steps of hiPSC culture and differentiation under chemically defined conditions. This streamlined approach allowed rapid and standardized manufacturing of billions of hiPSCs that can be produced in parallel from up to 90 different patient-and disease-specific cell lines. Moreover, we established automated multi-lineage differentiation to generate primary embryonic germ layers and more mature phenotypes such as neurons, cardiomyocytes, and hepatocytes. To validate our approach, we carefully compared robotic and manual cell culture and performed molecular and functional cell characterizations (e.g. bulk culture and single-cell transcriptomics, mass cytometry, metabolism, electrophysiology, Zika virus experiments) in order to benchmark industrial-scale cell culture operations towards building an integrated platform for efficient cell manufacturing for disease modeling, drug screening, and cell therapy. Combining stem cell-based models and non-stop robotic cell culture may become a powerful strategy to increase scientific rigor and productivity, which are particularly important during public health emergencies (e.g. opioid crisis, COVID-19 pandemic).
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Affiliation(s)
- Carlos A. Tristan
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Pinar Ormanoglu
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Jaroslav Slamecka
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Claire Malley
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Pei-Hsuan Chu
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Vukasin M. Jovanovic
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Yeliz Gedik
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Charles Bonney
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Elena Barnaeva
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - John Braisted
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | | | - Dorjbal Dorjsuren
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Michael J. Iannotti
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Ty C. Voss
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Sam Michael
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Ilyas Singeç
- National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), Rockville, MD 20850, USA
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28
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Halliwell JA, Frith TJR, Laing O, Price CJ, Bower OJ, Stavish D, Gokhale PJ, Hewitt Z, El-Khamisy SF, Barbaric I, Andrews PW. Nucleosides Rescue Replication-Mediated Genome Instability of Human Pluripotent Stem Cells. Stem Cell Reports 2020; 14:1009-1017. [PMID: 32413278 PMCID: PMC7355123 DOI: 10.1016/j.stemcr.2020.04.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/14/2020] [Accepted: 04/14/2020] [Indexed: 12/20/2022] Open
Abstract
Human pluripotent stem cells (PSCs) are subject to the appearance of recurrent genetic variants on prolonged culture. We have now found that, compared with isogenic differentiated cells, PSCs exhibit evidence of considerably more DNA damage during the S phase of the cell cycle, apparently as a consequence of DNA replication stress marked by slower progression of DNA replication, activation of latent origins of replication, and collapse of replication forks. As in many cancers, which, like PSCs, exhibit a shortened G1 phase and DNA replication stress, the resulting DNA damage may underlie the higher incidence of abnormal and abortive mitoses in PSCs, resulting in chromosomal non-dysjunction or cell death. However, we have found that the extent of DNA replication stress, DNA damage, and consequent aberrant mitoses can be substantially reduced by culturing PSCs in the presence of exogenous nucleosides, resulting in improved survival, clonogenicity, and population growth.
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Affiliation(s)
- Jason A Halliwell
- Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Thomas J R Frith
- Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Owen Laing
- Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Christopher J Price
- Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Oliver J Bower
- Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Dylan Stavish
- Department of Biomedical Science, 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
| | - Zoe Hewitt
- Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Sherif F El-Khamisy
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Ivana Barbaric
- Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield S10 2TN, UK.
| | - Peter W Andrews
- Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield S10 2TN, UK.
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29
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Lau KX, Mason EA, Kie J, De Souza DP, Kloehn J, Tull D, McConville MJ, Keniry A, Beck T, Blewitt ME, Ritchie ME, Naik SH, Zalcenstein D, Korn O, Su S, Romero IG, Spruce C, Baker CL, McGarr TC, Wells CA, Pera MF. Unique properties of a subset of human pluripotent stem cells with high capacity for self-renewal. Nat Commun 2020; 11:2420. [PMID: 32415101 PMCID: PMC7229198 DOI: 10.1038/s41467-020-16214-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 04/16/2020] [Indexed: 01/06/2023] Open
Abstract
Archetypal human pluripotent stem cells (hPSC) are widely considered to be equivalent in developmental status to mouse epiblast stem cells, which correspond to pluripotent cells at a late post-implantation stage of embryogenesis. Heterogeneity within hPSC cultures complicates this interspecies comparison. Here we show that a subpopulation of archetypal hPSC enriched for high self-renewal capacity (ESR) has distinct properties relative to the bulk of the population, including a cell cycle with a very low G1 fraction and a metabolomic profile that reflects a combination of oxidative phosphorylation and glycolysis. ESR cells are pluripotent and capable of differentiation into primordial germ cell-like cells. Global DNA methylation levels in the ESR subpopulation are lower than those in mouse epiblast stem cells. Chromatin accessibility analysis revealed a unique set of open chromatin sites in ESR cells. RNA-seq at the subpopulation and single cell levels shows that, unlike mouse epiblast stem cells, the ESR subset of hPSC displays no lineage priming, and that it can be clearly distinguished from gastrulating and extraembryonic cell populations in the primate embryo. ESR hPSC correspond to an earlier stage of post-implantation development than mouse epiblast stem cells. Human pluripotent cells (hPSCs) in standard culture are similar to mouse epiblast cells, but heterogeneity within hPSC cultures complicates comparisons. Here the authors show that a subpopulation of hPSCs enriched for self-renewal capacity have distinct cell cycle, metabolic, DNA methylation, and ATAC-seq profiles.
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Affiliation(s)
- Kevin X Lau
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Elizabeth A Mason
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Joshua Kie
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - David P De Souza
- Metabolomics Australia, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Joachim Kloehn
- Department of Biochemistry and Molecular Biology, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Dedreia Tull
- Metabolomics Australia, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Malcolm J McConville
- Metabolomics Australia, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, 3052, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Andrew Keniry
- Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Tamara Beck
- Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia
| | - Marnie E Blewitt
- Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Matthew E Ritchie
- Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia
| | - Shalin H Naik
- Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia
| | - Daniela Zalcenstein
- Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia
| | - Othmar Korn
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Shian Su
- Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia
| | - Irene Gallego Romero
- Melbourne Integrative Genomics, School of Biosciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | | | | | | | - Christine A Wells
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Divisions of Cancer and Hematology and Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia
| | - Martin F Pera
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, 3010, Australia. .,Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia. .,The Jackson Laboratory, Bar Harbor, ME, 04609, USA. .,The Florey Institute of Neuroscience and Mental Health, 30 Royal Parade, Parkville, Victoria, 3052, Australia.
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30
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Thompson O, von Meyenn F, Hewitt Z, Alexander J, Wood A, Weightman R, Gregory S, Krueger F, Andrews S, Barbaric I, Gokhale PJ, Moore HD, Reik W, Milo M, Nik-Zainal S, Yusa K, Andrews PW. Low rates of mutation in clinical grade human pluripotent stem cells under different culture conditions. Nat Commun 2020; 11:1528. [PMID: 32251294 PMCID: PMC7089967 DOI: 10.1038/s41467-020-15271-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 02/24/2020] [Indexed: 12/15/2022] Open
Abstract
The occurrence of repetitive genomic changes that provide a selective growth advantage in pluripotent stem cells is of concern for their clinical application. However, the effect of different culture conditions on the underlying mutation rate is unknown. Here we show that the mutation rate in two human embryonic stem cell lines derived and banked for clinical application is low and not substantially affected by culture with Rho Kinase inhibitor, commonly used in their routine maintenance. However, the mutation rate is reduced by >50% in cells cultured under 5% oxygen, when we also found alterations in imprint methylation and reversible DNA hypomethylation. Mutations are evenly distributed across the chromosomes, except for a slight increase on the X-chromosome, and an elevation in intergenic regions suggesting that chromatin structure may affect mutation rate. Overall the results suggest that pluripotent stem cells are not subject to unusually high rates of genetic or epigenetic alterations.
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Affiliation(s)
- Oliver Thompson
- The Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Ferdinand von Meyenn
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK
- Institute of Food, Nutrition and Health, ETH Zurich, 8603, Schwerzenbach, Switzerland
| | - Zoe Hewitt
- The Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - John Alexander
- The Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Andrew Wood
- The Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Richard Weightman
- The Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Sian Gregory
- The Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Felix Krueger
- Bioinformatics Group, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Simon Andrews
- Bioinformatics Group, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Ivana Barbaric
- The Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Paul J Gokhale
- The Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Harry D Moore
- The Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Marta Milo
- The Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Serena Nik-Zainal
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Academic Laboratory of Medical Genetics, Cambridge University Hospitals NHS Foundation Trust, Box 238, Lv6 Addenbrooke' Treatment Centre, Cambridge Biomedical Research Campus, Cambridge, CB2 0QQ, UK
- MRC Cancer Unit, University of Cambridge, Hutchinson/MRC Research Centre, Box 1297, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Kosuke Yusa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan.
| | - Peter W Andrews
- The Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
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31
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The recent advances in the mathematical modelling of human pluripotent stem cells. SN APPLIED SCIENCES 2020; 2:276. [PMID: 32803125 PMCID: PMC7391994 DOI: 10.1007/s42452-020-2070-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 01/17/2020] [Indexed: 12/20/2022] Open
Abstract
Human pluripotent stem cells hold great promise for developments in regenerative medicine and drug design. The mathematical modelling of stem cells and their properties is necessary to understand and quantify key behaviours and develop non-invasive prognostic modelling tools to assist in the optimisation of laboratory experiments. Here, the recent advances in the mathematical modelling of hPSCs are discussed, including cell kinematics, cell proliferation and colony formation, and pluripotency and differentiation.
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32
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Kinoshita K, Munesue T, Toki F, Isshiki M, Higashiyama S, Barrandon Y, Nishimura EK, Yanagihara Y, Nanba D. Automated collective motion analysis validates human keratinocyte stem cell cultures. Sci Rep 2019; 9:18725. [PMID: 31822757 PMCID: PMC6904747 DOI: 10.1038/s41598-019-55279-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 11/26/2019] [Indexed: 01/03/2023] Open
Abstract
Identification and quality assurance of stem cells cultured in heterogeneous cell populations are indispensable for successful stem cell therapy. Here we present an image-processing pipeline for automated identification and quality assessment of human keratinocyte stem cells. When cultivated under appropriate conditions, human epidermal keratinocyte stem cells give rise to colonies and exhibit higher locomotive capacity as well as significant proliferative potential. Image processing and kernel density estimation were used to automatically extract the area of keratinocyte colonies from phase-contrast images of cultures containing feeder cells. The DeepFlow algorithm was then used to calculate locomotion speed of the colony area by analyzing serial images. This image-processing pipeline successfully identified keratinocyte stem cell colonies by measuring cell locomotion speed, and also assessed the effect of oligotrophic culture conditions and chemical inhibitors on keratinocyte behavior. Therefore, this study provides automated procedures for image-based quality control of stem cell cultures and high-throughput screening of small molecules targeting stem cells.
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Affiliation(s)
- Koji Kinoshita
- Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan.
| | - Takuya Munesue
- Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan
| | - Fujio Toki
- Department of Stem Cell Biology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Masaharu Isshiki
- Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan
| | - Shigeki Higashiyama
- Division of Cell Growth and Tumor Regulation, Proteo-Science Center, Ehime University, Shitsukawa, Toon, Ehime, 791-0295, Japan.,Department of Biochemistry and Molecular Genetics, Ehime University Graduate School of Medicine, Toon, Shitsukawa, Ehime, 791-0295, Japan
| | - Yann Barrandon
- Institute of Medical Biology, A*STAR, Duke-NUS Graduate Medical School, and Department of Plastic, Reconstructive and Aesthetic Surgery, Singapore General Hospital, Singapore
| | - Emi K Nishimura
- Department of Stem Cell Biology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Yoshio Yanagihara
- Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan
| | - Daisuke Nanba
- Department of Stem Cell Biology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
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33
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Quantification of the morphological characteristics of hESC colonies. Sci Rep 2019; 9:17569. [PMID: 31772193 PMCID: PMC6879623 DOI: 10.1038/s41598-019-53719-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 11/04/2019] [Indexed: 11/25/2022] Open
Abstract
The maintenance of the undifferentiated state in human embryonic stem cells (hESCs) is critical for further application in regenerative medicine, drug testing and studies of fundamental biology. Currently, the selection of the best quality cells and colonies for propagation is typically performed by eye, in terms of the displayed morphological features, such as prominent/abundant nucleoli and a colony with a tightly packed appearance and a well-defined edge. Using image analysis and computational tools, we precisely quantify these properties using phase-contrast images of hESC colonies of different sizes (0.1–1.1 \documentclass[12pt]{minimal}
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\begin{document}$${{\bf{\text{mm}}}}^{{\bf{2}}}$$\end{document}mm2) during days 2, 3 and 4 after plating. Our analyses reveal noticeable differences in their structure influenced directly by the colony area \documentclass[12pt]{minimal}
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\begin{document}$${\boldsymbol{A}}$$\end{document}A. Large colonies (A > 0.6 mm2) have cells with smaller nuclei and a short intercellular distance when compared with small colonies (A < 0.2 mm2). The gaps between the cells, which are present in small and medium sized colonies with A ≤ 0.6 mm2, disappear in large colonies (A > 0.6 mm2) due to the proliferation of the cells in the bulk. This increases the colony density and the number of nearest neighbours. We also detect the self-organisation of cells in the colonies where newly divided (smallest) cells cluster together in patches, separated from larger cells at the final stages of the cell cycle. This might influence directly cell-to-cell interactions and the community effects within the colonies since the segregation induced by size differences allows the interchange of neighbours as the cells proliferate and the colony grows. Our findings are relevant to efforts to determine the quality of hESC colonies and establish colony characteristics database.
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Abstract
Human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs) have promising clinical applications which often rely on clonally-homogeneous cell populations. To achieve this, it is important to ensure that each colony originates from a single founding cell and to avoid subsequent merging of colonies during their growth. Clonal homogeneity can be obtained with low seeding densities; however, this leads to low yield and viability. It is therefore important to quantitatively assess how seeding density affects clonality loss so that experimental protocols can be optimised to meet the required standards. Here we develop a quantitative framework for modelling the growth of hESC colonies from a given seeding density based on stochastic exponential growth. This allows us to identify the timescales for colony merges and over which colony size no longer predicts the number of founding cells. We demonstrate the success of our model by applying it to our own experiments of hESC colony growth; while this is based on a particular experimental set-up, the model can be applied more generally to other cell lines and experimental conditions to predict these important timescales.
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35
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Nikitina TV, Kashevarova AA, Lebedev IN. Chromosomal Instability and Karyotype Correction in Human Induced Pluripotent Stem Cells. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419100090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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36
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Laing O, Halliwell J, Barbaric I. Rapid PCR Assay for Detecting Common Genetic Variants Arising in Human Pluripotent Stem Cell Cultures. ACTA ACUST UNITED AC 2019; 49:e83. [PMID: 30821932 DOI: 10.1002/cpsc.83] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Human pluripotent stem cells (hPSCs) are prone to acquiring genetic changes upon prolonged culture. Particularly common are copy number changes, including gains of chromosomes 1q, 12p, 17q, and 20q, and/or loss of chromosomes 10p and 18q. The variant cells harboring common genetic changes display altered behaviors compared to their diploid counterparts, thus potentially impacting upon the validity of experimental results and safety of hPSC-derived cellular therapies. Hence, a critical quality attribute in hPSC maintenance should include frequent monitoring for genetic changes arising in cultures. This in turn places large demands on the genotyping assays for detection of genetic changes. Traditional methods for screening cells entail specialized cytogenetic analyses, but their high costs and a lengthy turnaround time make them impractical for high-throughput analyses and routine laboratory use. Here, we detail a protocol for a rapid, accessible, and affordable PCR-based method for detection of frequently occurring copy number changes in hPSCs. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Owen Laing
- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Sheffield, United Kingdom
| | - Jason Halliwell
- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Sheffield, United Kingdom
| | - Ivana Barbaric
- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Sheffield, United Kingdom
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37
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Stacey GN, Andrews PW, Barbaric I, Boiers C, Chandra A, Cossu G, Csontos L, Frith TJ, Halliwell JA, Hewitt Z, McCall M, Moore HD, Parmar M, Panico MB, Pisupati V, Shichkin VP, Stacey AR, Tedesco FS, Thompson O, Wagey R. Stem cell culture conditions and stability: a joint workshop of the PluriMes Consortium and Pluripotent Stem Cell Platform. Regen Med 2019; 14:243-255. [PMID: 30938271 PMCID: PMC7611410 DOI: 10.2217/rme-2019-0001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Human stem cells have the potential to transform medicine. However, hurdles remain to ensure that manufacturing processes produce safe and effective products. A thorough understanding of the biological processes occurring during manufacture is fundamental to assuring these qualities and thus, their acceptability to regulators and clinicians. Leaders in both human pluripotent and somatic stem cells, were brought together with experts in clinical translation, biomanufacturing and regulation, to discuss key issues in assuring appropriate manufacturing conditions for delivery of effective and safe products from these cell types. This report summarizes the key issues discussed and records consensus reached by delegates and emphasizes the need for accurate language and nomenclature in the scientific discourse around stem cells.
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Affiliation(s)
- Glyn N Stacey
- International Stem Cell Banking Initiative, 2 High Street, Barley, Hertfordshire SG8 8HZ, UK
| | - Peter W Andrews
- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Sheffield, S10 2TN, UK
| | - Ivana Barbaric
- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Sheffield, S10 2TN, UK
| | - Charlotta Boiers
- Department of Cancer Biology, University College London, London, WC1E 6DD, UK
- Cancer Institute, University College London, London, WC1E 6DD, UK
| | | | - Giulio Cossu
- Division of Cell Matrix Biology & Regenerative Medicine, University of Manchester, M13 9PL, UK
| | | | - Thomas Jr Frith
- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Sheffield, S10 2TN, UK
| | - Jason A Halliwell
- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Sheffield, S10 2TN, UK
| | - Zoe Hewitt
- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Sheffield, S10 2TN, UK
| | - Mark McCall
- Centre for Biological Engineering, Loughborough University, Loughborough, LE11 3TU, UK
| | - Harry D Moore
- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Sheffield, S10 2TN, UK
| | - Malin Parmar
- Developmental & Regenerative Neurobiology, Department of Experimental Medical Science, Wallenberg Neuroscience Center, Lund, S221 84, Sweden
- Lund Stem Cell Center, Lund University, Lund, S221 84, Sweden
| | - M Beatrice Panico
- Medicines & Healthcare products Regulatory Agency, London, E14 4PU, UK
| | - Venkat Pisupati
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, CB2 0PY, UK
| | - Valentin P Shichkin
- Research Centre of Immunology & Biomedical Technologies, Open International University of Human Development Ukraine, Kyiv 03115, Ukraine
- Bienta Ltd, 78 Chervonotkatska Str., Kyiv 02094, Ukraine
| | - Alison R Stacey
- Division of Cell Matrix Biology & Regenerative Medicine, University of Manchester, M13 9PL, UK
| | - Francesco S Tedesco
- Department of Cell & Developmental Biology & Great Ormond Street Institute of Child Health, University College London, WC1E 6DE, UK
- The Dubowitz Neuromuscular Centre, Greta Ormond Street Institute of Child Health, University College London, WC1N 1EH, London, UK
| | - Oliver Thompson
- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Sheffield, S10 2TN, UK
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38
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Zhang J, Hirst AJ, Duan F, Qiu H, Huang R, Ji Y, Bai L, Zhang F, Robinson D, Jones M, Li L, Wang P, Jiang P, Andrews PW, Barbaric I, Na J. Anti-apoptotic Mutations Desensitize Human Pluripotent Stem Cells to Mitotic Stress and Enable Aneuploid Cell Survival. Stem Cell Reports 2019; 12:557-571. [PMID: 30773485 PMCID: PMC6411485 DOI: 10.1016/j.stemcr.2019.01.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 01/17/2019] [Accepted: 01/17/2019] [Indexed: 12/22/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) are susceptible to numerical and structural chromosomal alterations during long-term culture. We show that mitotic errors occur frequently in hPSCs and that prometaphase arrest leads to very rapid apoptosis in undifferentiated but not in differentiated cells. hPSCs express high levels of proapoptotic protein NOXA in undifferentiated state. Knocking out NOXA by CRISPR or upregulation of the anti-apoptosis gene BCL-XL significantly reduced mitotic cell death, allowing the survival of aneuploid cells and the formation of teratomas significantly larger than their wild-type parental hPSCs. These results indicate that the normally low threshold of apoptosis in hPSCs can safeguard their genome integrity by clearing cells undergoing abnormal division. The amplification of BCL2L1 on chromosome 20q11.21, a frequent mutation in hPSCs, although not directly oncogenic, reduces the sensitivity of hPSCs to damage caused by erroneous mitosis and increases the risk of gaining aneuploidy.
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Affiliation(s)
- Jing Zhang
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Adam J Hirst
- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Sheffield S10 2TN, UK
| | - Fuyu Duan
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Hui Qiu
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Rujin Huang
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ying Ji
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Lufeng Bai
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Fengzhi Zhang
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Darren Robinson
- Light Microscopy Facility, Department of Biomedical Science, The University of Sheffield, Sheffield S10 2TN, UK
| | - Mark Jones
- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Sheffield S10 2TN, UK
| | - Le Li
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Peizhe Wang
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Peng Jiang
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Peter W Andrews
- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Sheffield S10 2TN, UK
| | - Ivana Barbaric
- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Sheffield S10 2TN, UK.
| | - Jie Na
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing 100084, China.
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39
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Hayashi Y, Ohnuma K, Furue MK. Pluripotent Stem Cell Heterogeneity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1123:71-94. [DOI: 10.1007/978-3-030-11096-3_6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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40
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Chang J, Kim MH, Agung E, Senda S, Kino-Oka M. Effect of migratory behaviors on human induced pluripotent stem cell colony formation on different extracellular matrix proteins. Regen Ther 2018; 10:27-35. [PMID: 30525068 PMCID: PMC6260426 DOI: 10.1016/j.reth.2018.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/10/2018] [Accepted: 10/23/2018] [Indexed: 01/10/2023] Open
Abstract
Introduction Understanding how extracellular matrix (ECM) protein composition regulates the process of human induced pluripotent stem cell (hiPSC) colony formation may facilitate the design of optimal cell culture environments. In this study, we investigated the effect of migratory behaviors on hiPSC colony formation on various ECM-coated surfaces. Methods To quantify how different ECM proteins affect migratory behavior during the colony formation process, single cells were seeded onto surfaces coated with varying concentrations of different ECM proteins. Cell behavior was monitored by time-lapse observation, and quantitative analysis of migration rates in relation to colony formation patterns was performed. Actin cytoskeleton, focal adhesions, and cell–cell interactions were detected by fluorescence microscopy. Results Time-lapse observations revealed that different mechanisms of colony formation were dependent upon the migratory behavior of cells on different ECM surfaces. HiPSCs formed tight colonies on concentrated ECM substrates, while coating with dilute concentrations of ECM yielded more motile cells and colonies capable of splitting into single cells or small clusters. Enhanced migration caused a reduction of cell–cell contacts that enabled splitting or merging between cells and cell clusters, consequently reducing the efficiency of clonal colony formation. High cell-to-cell variability in migration responses to ECM surfaces elicited differential focal adhesion formation and E-cadherin expression within cells and colonies. This resulted in variability within focal adhesions and further loss of E-cadherin expression by hiPSCs. Conclusions Migration is an important factor affecting hiPSC colony-forming patterns. Regulation of migratory behavior can be an effective way to improve the expansion of hiPSCs while improving the process of clonal colony formation. We believe that this investigation provides a valuable method for understanding cell phenotypes and heterogeneity during colony formation in culture. hiPSC colony-forming patterns were dependent on migratory behavior on different ECM surfaces. Colony formation without splitting during migration improved efficiency of clonal colony formation. Variability in migration behavior elicited differential cytoskeletal formation and E-cadherin expression. Our method is valuable for understanding cell phenotypes and heterogeneity during colony formation.
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Affiliation(s)
- Jessica Chang
- Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, 210-8681 Japan
| | - Mee-Hae Kim
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Eviryanti Agung
- Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, 210-8681 Japan
| | - Sho Senda
- Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, 210-8681 Japan
| | - Masahiro Kino-Oka
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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41
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Ae Park M, Sun Jung H, Slukvin I. Genetic Engineering of Human Pluripotent Stem Cells Using PiggyBac Transposon System. CURRENT PROTOCOLS IN STEM CELL BIOLOGY 2018; 47:e63. [PMID: 30281932 PMCID: PMC6212322 DOI: 10.1002/cpsc.63] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Human pluripotent stem cells (hPSCs) emerged as an important tool to investigate human development and disease. These studies often require genetically engineering hPSCs to stably express a transgene, which remains functional in various hPSC progeny. PiggyBac transposon is a highly effective and technically simple vector system with large cargo space available for permanent gene delivery. This unit describes the use of PiggyBac transposons to genetically engineer hPSCs to introduce conditionally expressed transgene or reporter to effectively monitor gene expression during differentiation. Both methods enable robust generation of stable hPSC lines within 1 month. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Mi Ae Park
- National Primate Research Center, University of Wisconsin Graduate School, 1220 Capitol Court, Madison, Wisconsin
| | - Ho Sun Jung
- National Primate Research Center, University of Wisconsin Graduate School, 1220 Capitol Court, Madison, Wisconsin
| | - Igor Slukvin
- National Primate Research Center, University of Wisconsin Graduate School, 1220 Capitol Court, Madison, Wisconsin
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
- Department of Pathology and Laboratory Medicine, University of Wisconsin Medical School, 600 Highland Avenue, Madison, Wisconsin
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42
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Yamamoto Y, Miyazaki S, Maruyama K, Kobayashi R, Le MNT, Kano A, Kondow A, Fujii S, Ohnuma K. Random migration of induced pluripotent stem cell-derived human gastrulation-stage mesendoderm. PLoS One 2018; 13:e0201960. [PMID: 30199537 PMCID: PMC6130871 DOI: 10.1371/journal.pone.0201960] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 07/25/2018] [Indexed: 01/03/2023] Open
Abstract
Gastrulation is the initial systematic deformation of the embryo to form germ layers, which is characterized by the placement of appropriate cells in their destined locations. Thus, gastrulation, which occurs at the beginning of the second month of pregnancy, is a critical stage in human body formation. Although histological analyses indicate that human gastrulation is similar to that of other amniotes (birds and mammals), much of human gastrulation dynamics remain unresolved due to ethical and technical limitations. We used human induced pluripotent stem cells (hiPSCs) to study the migration of mesendodermal cells through the primitive streak to form discoidal germ layers during gastrulation. Immunostaining results showed that hiPSCs differentiated into mesendodermal cells and that epithelial–mesenchymal transition occurred through the activation of the Activin/Nodal and Wnt/beta-catenin pathways. Single-cell time-lapse imaging of cells adhered to cover glass showed that mesendodermal differentiation resulted in the dissociation of cells and an increase in their migration speed, thus confirming the occurrence of epithelial–mesenchymal transition. These results suggest that mesendodermal cells derived from hiPSCs may be used as a model system for studying migration during human gastrulation in vitro. Using random walk analysis, we found that random migration occurred for both undifferentiated hiPSCs and differentiated mesendodermal cells. Two-dimensional random walk simulation showed that homogeneous dissociation of particles may form a discoidal layer, suggesting that random migration might be suitable to effectively disperse cells homogeneously from the primitive streak to form discoidal germ layers during human gastrulation.
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Affiliation(s)
- Yuta Yamamoto
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, NIIGATA, Japan
| | - Shota Miyazaki
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, NIIGATA, Japan
| | - Kenshiro Maruyama
- Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, NIIGATA, Japan
| | - Ryo Kobayashi
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, NIIGATA, Japan
| | - Minh Nguyen Tuyet Le
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, NIIGATA, Japan
| | - Ayumu Kano
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, NIIGATA, Japan
| | - Akiko Kondow
- Division of Biomedical Polymer Science, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi, Japan
| | - Shuji Fujii
- Department of Materials Science and Technology, Nagaoka University of Technology, Nagaoka, NIIGATA, Japan
| | - Kiyoshi Ohnuma
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, NIIGATA, Japan
- Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, NIIGATA, Japan
- * E-mail:
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43
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Wadkin LE, Orozco-Fuentes S, Neganova I, Swan G, Laude A, Lako M, Shukurov A, Parker NG. Correlated random walks of human embryonic stem cells in vitro. Phys Biol 2018; 15:056006. [DOI: 10.1088/1478-3975/aac008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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44
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Cancer: a CINful evolution. Curr Opin Cell Biol 2018; 52:136-144. [DOI: 10.1016/j.ceb.2018.03.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 03/06/2018] [Accepted: 03/21/2018] [Indexed: 12/12/2022]
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45
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Allison TF, Smith AJH, Anastassiadis K, Sloane-Stanley J, Biga V, Stavish D, Hackland J, Sabri S, Langerman J, Jones M, Plath K, Coca D, Barbaric I, Gokhale P, Andrews PW. Identification and Single-Cell Functional Characterization of an Endodermally Biased Pluripotent Substate in Human Embryonic Stem Cells. Stem Cell Reports 2018; 10:1895-1907. [PMID: 29779895 PMCID: PMC5993559 DOI: 10.1016/j.stemcr.2018.04.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 04/17/2018] [Accepted: 04/17/2018] [Indexed: 11/28/2022] Open
Abstract
Human embryonic stem cells (hESCs) display substantial heterogeneity in gene expression, implying the existence of discrete substates within the stem cell compartment. To determine whether these substates impact fate decisions of hESCs we used a GFP reporter line to investigate the properties of fractions of putative undifferentiated cells defined by their differential expression of the endoderm transcription factor, GATA6, together with the hESC surface marker, SSEA3. By single-cell cloning, we confirmed that substates characterized by expression of GATA6 and SSEA3 include pluripotent stem cells capable of long-term self-renewal. When clonal stem cell colonies were formed from GATA6-positive and GATA6-negative cells, more of those derived from GATA6-positive cells contained spontaneously differentiated endoderm cells than similar colonies derived from the GATA6-negative cells. We characterized these discrete cellular states using single-cell transcriptomic analysis, identifying a potential role for SOX17 in the establishment of the endoderm-biased stem cell state. Subsets of hESCs can co-express pluripotency-associated and lineage-specific genes hESCs co-expressing GATA6 are capable of long-term self-renewal Single GATA6-expressing hESCs regenerate GATA6-negative cells GATA6-expressing hESCs are biased in their propensity for differentiation
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Affiliation(s)
- Thomas F Allison
- Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, UK.
| | - Andrew J H Smith
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH16 4UU, UK; MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | | | - Jackie Sloane-Stanley
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Veronica Biga
- Signal Processing and Complex Systems Group, Department of Automatic Control and Systems Engineering, University of Sheffield, Sheffield S10 2TN, UK; School of Medicine, Faculty of Biology and Health, University of Manchester, Manchester M13 9PT, UK
| | - Dylan Stavish
- Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, UK
| | - James Hackland
- Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, UK
| | - Shan Sabri
- UCLA School of Medicine, Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Justin Langerman
- UCLA School of Medicine, Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Mark Jones
- Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, UK
| | - Kathrin Plath
- UCLA School of Medicine, Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Daniel Coca
- Signal Processing and Complex Systems Group, Department of Automatic Control and Systems Engineering, University of Sheffield, Sheffield S10 2TN, UK
| | - Ivana Barbaric
- Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, UK
| | - Paul Gokhale
- Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, UK
| | - Peter W Andrews
- Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, UK
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46
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Mitchell R, Molligan J, Rooney S, Cho Y, Schon L, Zhang Z. Functionally compromised synovium-derived mesenchymal stem cells in Charcot neuroarthropathy. Exp Mol Pathol 2018; 104:82-88. [DOI: 10.1016/j.yexmp.2018.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 01/10/2018] [Indexed: 10/18/2022]
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47
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Nava-Sedeño JM, Hatzikirou H, Klages R, Deutsch A. Cellular automaton models for time-correlated random walks: derivation and analysis. Sci Rep 2017; 7:16952. [PMID: 29209065 PMCID: PMC5717221 DOI: 10.1038/s41598-017-17317-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/22/2017] [Indexed: 11/09/2022] Open
Abstract
Many diffusion processes in nature and society were found to be anomalous, in the sense of being fundamentally different from conventional Brownian motion. An important example is the migration of biological cells, which exhibits non-trivial temporal decay of velocity autocorrelation functions. This means that the corresponding dynamics is characterized by memory effects that slowly decay in time. Motivated by this we construct non-Markovian lattice-gas cellular automata models for moving agents with memory. For this purpose the reorientation probabilities are derived from velocity autocorrelation functions that are given a priori; in that respect our approach is “data-driven”. Particular examples we consider are velocity correlations that decay exponentially or as power laws, where the latter functions generate anomalous diffusion. The computational efficiency of cellular automata combined with our analytical results paves the way to explore the relevance of memory and anomalous diffusion for the dynamics of interacting cell populations, like confluent cell monolayers and cell clustering.
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Affiliation(s)
- J M Nava-Sedeño
- Technische Universität Dresden, Center for Information Services and High Performance Computing, Nöthnitzer Straße 46, 01062, Dresden, Germany.
| | - H Hatzikirou
- Technische Universität Dresden, Center for Information Services and High Performance Computing, Nöthnitzer Straße 46, 01062, Dresden, Germany.,Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Center for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - R Klages
- School of Mathematical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, United Kingdom
| | - A Deutsch
- Technische Universität Dresden, Center for Information Services and High Performance Computing, Nöthnitzer Straße 46, 01062, Dresden, Germany
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48
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Baker D, Hirst AJ, Gokhale PJ, Juarez MA, Williams S, Wheeler M, Bean K, Allison TF, Moore HD, Andrews PW, Barbaric I. Detecting Genetic Mosaicism in Cultures of Human Pluripotent Stem Cells. Stem Cell Reports 2017; 7:998-1012. [PMID: 27829140 PMCID: PMC5106530 DOI: 10.1016/j.stemcr.2016.10.003] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 10/10/2016] [Accepted: 10/10/2016] [Indexed: 02/07/2023] Open
Abstract
Genetic changes in human pluripotent stem cells (hPSCs) gained during culture can confound experimental results and potentially jeopardize the outcome of clinical therapies. Particularly common changes in hPSCs are trisomies of chromosomes 1, 12, 17, and 20. Thus, hPSCs should be regularly screened for such aberrations. Although a number of methods are used to assess hPSC genotypes, there has been no systematic evaluation of the sensitivity of the commonly used techniques in detecting low-level mosaicism in hPSC cultures. We have performed mixing experiments to mimic the naturally occurring mosaicism and have assessed the sensitivity of chromosome banding, qPCR, fluorescence in situ hybridization, and digital droplet PCR in detecting variants. Our analysis highlights the limits of mosaicism detection by the commonly employed methods, a pivotal requirement for interpreting the genetic status of hPSCs and for setting standards for safe applications of hPSCs in regenerative medicine. hPSCs conform to random sampling rules used for karyotyping Excluding mosaicism at <1% level requires sampling >500 metaphases qPCR is a rapid assay for detection of commonly amplified regions in hPSCs Cultures scored as normal by commonly used methods could harbor up to 10% variants
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Affiliation(s)
- Duncan Baker
- Department of Biomedical Science, Centre for Stem Cell Biology, The University of Sheffield, Sheffield S10 2TN, UK; Sheffield Diagnostic Genetic Services, Sheffield Children's Hospital, Sheffield S10 2TH, UK
| | - Adam J Hirst
- Department of Biomedical Science, Centre for Stem Cell Biology, The University of Sheffield, Sheffield S10 2TN, UK
| | - Paul J Gokhale
- Department of Biomedical Science, Centre for Stem Cell Biology, The University of Sheffield, Sheffield S10 2TN, UK
| | - Miguel A Juarez
- School of Mathematics and Statistics, The University of Sheffield, Sheffield S3 7RH, UK
| | - Steve Williams
- Sheffield Diagnostic Genetic Services, Sheffield Children's Hospital, Sheffield S10 2TH, UK
| | - Mark Wheeler
- Sheffield Diagnostic Genetic Services, Sheffield Children's Hospital, Sheffield S10 2TH, UK
| | - Kerry Bean
- Sheffield Diagnostic Genetic Services, Sheffield Children's Hospital, Sheffield S10 2TH, UK
| | - Thomas F Allison
- Department of Biomedical Science, Centre for Stem Cell Biology, The University of Sheffield, Sheffield S10 2TN, UK
| | - Harry D Moore
- Department of Biomedical Science, Centre for Stem Cell Biology, The University of Sheffield, Sheffield S10 2TN, UK
| | - Peter W Andrews
- Department of Biomedical Science, Centre for Stem Cell Biology, The University of Sheffield, Sheffield S10 2TN, UK
| | - Ivana Barbaric
- Department of Biomedical Science, Centre for Stem Cell Biology, The University of Sheffield, Sheffield S10 2TN, UK.
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49
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Martin U. Genome stability of programmed stem cell products. Adv Drug Deliv Rev 2017; 120:108-117. [PMID: 28917518 DOI: 10.1016/j.addr.2017.09.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 08/31/2017] [Accepted: 09/07/2017] [Indexed: 01/23/2023]
Abstract
Inherited and acquired genomic abnormalities are known to cause genetic diseases and contribute to cancer formation. Recent studies demonstrated a substantial mutational load in mouse and human embryonic and induced pluripotent stem cells (ESCs and iPSCs). Single nucleotide variants, copy number variations, and larger chromosomal abnormalities may influence the differentiation capacity of pluripotent stem cells and the functionality of their derivatives in disease modeling and drug screening, and are considered a serious risk for cellular therapies based on ESC or iPSC derivatives. This review discusses the types and origins of different genetic abnormalities in pluripotent stem cells, methods for their detection, and the mechanisms of development and enrichment during reprogramming and culture expansion.
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Affiliation(s)
- Ulrich Martin
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH Cluster of Excellence, German Center for Lung Research, Hannover Medical School, Germany.
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50
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McClelland SE. Role of chromosomal instability in cancer progression. Endocr Relat Cancer 2017; 24:T23-T31. [PMID: 28696210 DOI: 10.1530/erc-17-0187] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 07/10/2017] [Indexed: 12/24/2022]
Abstract
Cancer cells often display chromosomal instability (CIN), a defect that involves loss or rearrangement of the cell's genetic material - chromosomes - during cell division. This process results in the generation of aneuploidy, a deviation from the haploid number of chromosomes, and structural alterations of chromosomes in over 90% of solid tumours and many haematological cancers. This trait is unique to cancer cells as normal cells in the body generally strictly maintain the correct number and structure of chromosomes. This key difference between cancer and normal cells has led to two important hypotheses: (i) cancer cells have had to overcome inherent barriers to changes in chromosomes that are not tolerated in non-cancer cells and (ii) CIN represents a cancer-specific target to allow the specific elimination of cancer cells from the body. To exploit these hypotheses and design novel approaches to treat cancer, a full understanding of the mechanisms driving CIN and how CIN contributes to cancer progression is required. Here, we will discuss the possible mechanisms driving chromosomal instability, how CIN may contribute to the progression at multiple stages of tumour evolution and possible future therapeutic directions based on targeting cancer chromosomal instability.
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