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Shirakawa J, Ntege EH, Takemura M, Miyamoto S, Kawano T, Sampei C, Kawabata H, Nakamura H, Sunami H, Hayata T, Shimizu Y. Exploring SSEA3 as an emerging biomarker for assessing the regenerative potential of dental pulp-derived stem cells. Regen Ther 2024; 26:71-79. [PMID: 38828011 PMCID: PMC11139766 DOI: 10.1016/j.reth.2024.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 04/30/2024] [Accepted: 05/09/2024] [Indexed: 06/05/2024] Open
Abstract
Background Human dental pulp-derived stem cells (hDPSCs) have emerged as a promising source for adult stem cell-based regenerative medicine. Stage-specific embryonic antigen 3 (SSEA3) is a cell surface marker associated with Multilineage-differentiating stress-enduring (Muse) cells, a subpopulation of human bone marrow-derived stem cells (hBMSCs), known for their potent regenerative potential and safety profile. In this study, we investigated the influence of the prolonged culture period and the number of culture passages on the regenerative capacity of hDPSCs and explored the association between SSEA3 expression and their regenerative abilities. Methods hDPSCs were isolated and cultured for up to 20 passages. Cell proliferation, migration, and osteogenic, adipogenic and neurogenic differentiation potential were assessed at passages 5, 10, and 20. Flow cytometry and immunofluorescence were employed to analyze SSEA3 expression. RNA sequencing (RNA-seq) was performed on SSEA3-positive and SSEA3-negative hDPSCs to identify differentially expressed genes and associated pathways. Results Our findings demonstrated a progressive decline in hDPSCs proliferation and migration capacity with increasing passage number. Conversely, cell size exhibited a positive correlation with passage number. Early passage hDPSCs displayed superior osteogenic and adipogenic differentiation potential. Notably, SSEA3 expression exhibited a significant negative correlation with passage numbers, reflecting the observed decline in differentiation capacity. RNA-seq analysis revealed distinct transcriptional profiles between SSEA3-positive and SSEA3-negative hDPSCs. SSEA3-positive cells displayed upregulation of genes associated with ectodermal differentiation and downregulation of genes involved in cell adhesion. Conclusions This study elucidates the impact of passaging on hDPSC behavior and suggests SSEA3 as a valuable biomarker for evaluating stemness and regenerative potential. SSEA3-positive hDPSCs, functionally analogous to Muse cells, represent a promising cell population for developing targeted regenerative therapies with potentially improved clinical outcomes.
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Affiliation(s)
- Jumpei Shirakawa
- Department of Oral and Maxillofacial Surgery, and Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nakagami, Nishihara, Okinawa 903-0215, Japan
| | - Edward H. Ntege
- Department of Oral and Maxillofacial Surgery, and Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nakagami, Nishihara, Okinawa 903-0215, Japan
- Department of Plastic and Reconstructive Surgery, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nakagami, Nishihara, Okinawa 903-0215, Japan
| | - Masuo Takemura
- Department of Oral and Maxillofacial Surgery, and Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nakagami, Nishihara, Okinawa 903-0215, Japan
| | - Sho Miyamoto
- Department of Oral Surgery, Sapporo Medical University School of Medicine, South 1 West 16, Chuo-ku, Sapporo, Hokkaido, 060-8543, Japan
| | - Toshihiro Kawano
- Department of Oral and Maxillofacial Surgery, and Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nakagami, Nishihara, Okinawa 903-0215, Japan
| | - Chisato Sampei
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences and Faculty of Pharmaceutical Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 287-8510, Japan
| | - Hayato Kawabata
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences and Faculty of Pharmaceutical Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 287-8510, Japan
| | - Hiroyuki Nakamura
- Department of Oral and Maxillofacial Surgery, and Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nakagami, Nishihara, Okinawa 903-0215, Japan
| | - Hiroshi Sunami
- Advanced Medical Research Center, Faculty of Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Nakagami, Okinawa, 903-0215, Japan
| | - Tadayoshi Hayata
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences and Faculty of Pharmaceutical Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 287-8510, Japan
| | - Yusuke Shimizu
- Department of Plastic and Reconstructive Surgery, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nakagami, Nishihara, Okinawa 903-0215, Japan
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2
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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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3
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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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4
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Dynamic cytosolic foci of DPPA4 in human pluripotent stem cells. Tissue Cell 2022; 78:101893. [DOI: 10.1016/j.tice.2022.101893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 07/28/2022] [Accepted: 08/06/2022] [Indexed: 11/23/2022]
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5
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Knock E, Julian LM. Building on a Solid Foundation: Adding Relevance and Reproducibility to Neurological Modeling Using Human Pluripotent Stem Cells. Front Cell Neurosci 2021; 15:767457. [PMID: 34867204 PMCID: PMC8637745 DOI: 10.3389/fncel.2021.767457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/20/2021] [Indexed: 11/25/2022] Open
Abstract
The brain is our most complex and least understood organ. Animal models have long been the most versatile tools available to dissect brain form and function; however, the human brain is highly distinct from that of standard model organisms. In addition to existing models, access to human brain cells and tissues is essential to reach new frontiers in our understanding of the human brain and how to intervene therapeutically in the face of disease or injury. In this review, we discuss current and developing culture models of human neural tissue, outlining advantages over animal models and key challenges that remain to be overcome. Our principal focus is on advances in engineering neural cells and tissue constructs from human pluripotent stem cells (PSCs), though primary human cell and slice culture are also discussed. By highlighting studies that combine animal models and human neural cell culture techniques, we endeavor to demonstrate that clever use of these orthogonal model systems produces more reproducible, physiological, and clinically relevant data than either approach alone. We provide examples across a range of topics in neuroscience research including brain development, injury, and cancer, neurodegenerative diseases, and psychiatric conditions. Finally, as testing of PSC-derived neurons for cell replacement therapy progresses, we touch on the advancements that are needed to make this a clinical mainstay.
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Affiliation(s)
- Erin Knock
- Research and Development, STEMCELL Technologies Inc., Vancouver, BC, Canada.,Department of Biological Sciences, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
| | - Lisa M Julian
- Department of Biological Sciences, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
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6
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Kim MH, Thanuthanakhun N, Fujimoto S, Kino-Oka M. Effect of initial seeding density on cell behavior-driven epigenetic memory and preferential lineage differentiation of human iPSCs. Stem Cell Res 2021; 56:102534. [PMID: 34530397 DOI: 10.1016/j.scr.2021.102534] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/22/2021] [Accepted: 09/03/2021] [Indexed: 10/20/2022] Open
Abstract
Understanding the cellular behavioral mechanisms underlying memory formation and maintenance in human induced pluripotent stem cell (hiPSC) culture provides key strategies for achieving stability and robustness of cell differentiation. Here, we show that changes in cell behavior-driven epigenetic memory of hiPSC cultures alter their pluripotent state and subsequent differentiation. Interestingly, pluripotency-associated genes were activated during the entire cell growth phases along with increased active modifications and decreased repressive modifications. This memory effect can last several days in the long-term stationary phase and was sustained in the aspect of cell behavioral changes after subculture. Further, changes in growth-related cell behavior were found to induce nucleoskeletal reorganization and active versus repressive modifications, thereby enabling hiPSCs to change their differentiation potential. Overall, we discuss the cell behavior-driven epigenetic memory induced by the culture environment, and the effect of previous memory on cell lineage specification in the process of hiPSC differentiation.
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Affiliation(s)
- Mee-Hae Kim
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Naruchit Thanuthanakhun
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shun Fujimoto
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, 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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7
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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: 31] [Impact Index Per Article: 10.3] [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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8
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Kim MH, Kino-Oka M. Mechanobiological conceptual framework for assessing stem cell bioprocess effectiveness. Biotechnol Bioeng 2021; 118:4537-4549. [PMID: 34460101 DOI: 10.1002/bit.27929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/22/2021] [Accepted: 08/27/2021] [Indexed: 12/12/2022]
Abstract
Fully realizing the enormous potential of stem cells requires developing efficient bioprocesses and optimizations founded in mechanobiological considerations. Here, we emphasize the importance of mechanotransduction as one of the governing principles of stem cell bioprocesses, underscoring the need to further explore the behavioral mechanisms involved in sensing mechanical cues and coordinating transcriptional responses. We identify the sources of intrinsic, extrinsic, and external noise in bioprocesses requiring further study, and discuss the criteria and indicators that may be used to assess and predict cell-to-cell variability resulting from environmental fluctuations. Specifically, we propose a conceptual framework to explain the impact of mechanical forces within the cellular environment, identify key cell state determinants in bioprocesses, and discuss downstream implementation challenges.
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Affiliation(s)
- Mee-Hae Kim
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
| | - Masahiro Kino-Oka
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
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9
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Role of a Heat Shock Transcription Factor and the Major Heat Shock Protein Hsp70 in Memory Formation and Neuroprotection. Cells 2021; 10:cells10071638. [PMID: 34210082 PMCID: PMC8305005 DOI: 10.3390/cells10071638] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/18/2021] [Accepted: 06/25/2021] [Indexed: 12/23/2022] Open
Abstract
Heat shock proteins (Hsps) represent the most evolutionarily ancient, conserved, and universal system for protecting cells and the whole body from various types of stress. Among Hsps, the group of proteins with a molecular weight of 70 kDa (Hsp70) plays a particularly important role. These proteins are molecular chaperones that restore the native conformation of partially denatured proteins after exposure to proteotoxic forms of stress and are critical for the folding and intracellular trafficking of de novo synthesized proteins under normal conditions. Hsp70s are expressed at high levels in the central nervous system (CNS) of various animals and protect neurons from various types of stress, including heat shock, hypoxia, and toxins. Numerous molecular and behavioral studies have indicated that Hsp70s expressed in the CNS are important for memory formation. These proteins contribute to the folding and transport of synaptic proteins, modulate signaling cascades associated with synaptic activation, and participate in mechanisms of neurotransmitter release. In addition, HSF1, a transcription factor that is activated under stress conditions and mediates Hsps transcription, is also involved in the transcription of genes encoding many synaptic proteins, whose levels are increased in neurons under stress and during memory formation. Thus, stress activates the molecular mechanisms of memory formation, thereby allowing animals to better remember and later avoid potentially dangerous stimuli. Finally, Hsp70 has significant protective potential in neurodegenerative diseases. Increasing the level of endogenous Hsp70 synthesis or injecting exogenous Hsp70 reduces neurodegeneration, stimulates neurogenesis, and restores memory in animal models of ischemia and Alzheimer’s disease. These findings allow us to consider recombinant Hsp70 and/or Hsp70 pharmacological inducers as potential drugs for use in the treatment of ischemic injury and neurodegenerative disorders.
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10
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Li C, Mills Z, Zheng Z. Novel cell sources for bone regeneration. MedComm (Beijing) 2021; 2:145-174. [PMID: 34766140 PMCID: PMC8491221 DOI: 10.1002/mco2.51] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/03/2020] [Accepted: 12/09/2020] [Indexed: 01/09/2023] Open
Abstract
A plethora of both acute and chronic conditions, including traumatic, degenerative, malignant, or congenital disorders, commonly induce bone disorders often associated with severe persisting pain and limited mobility. Over 1 million surgical procedures involving bone excision, bone grafting, and fracture repair are performed each year in the U.S. alone, resulting in immense levels of public health challenges and corresponding financial burdens. Unfortunately, the innate self-healing capacity of bone is often inadequate for larger defects over a critical size. Moreover, as direct transplantation of committed osteoblasts is hindered by deficient cell availability, limited cell spreading, and poor survivability, an urgent need for novel cell sources for bone regeneration is concurrent. Thanks to the development in stem cell biology and cell reprogramming technology, many multipotent and pluripotent cells that manifest promising osteogenic potential are considered the regenerative remedy for bone defects. Considering these cells' investigation is still in its relative infancy, each of them offers their own particular challenges that must be conquered before the large-scale clinical application.
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Affiliation(s)
- Chenshuang Li
- Department of Orthodontics, School of Dental MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Zane Mills
- College of DentistryUniversity of OklahomaOklahoma CityOklahomaUSA
| | - Zhong Zheng
- Division of Growth and Development, School of DentistryUniversity of CaliforniaLos AngelesCaliforniaUSA
- Department of Surgery, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCaliforniaUSA
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11
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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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12
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Mus LM, Van Haver S, Popovic M, Trypsteen W, Lefever S, Zeltner N, Ogando Y, Jacobs EZ, Denecker G, Sanders E, Van Neste C, Vanhauwaert S, Decaesteker B, Deforce D, Van Nieuwerburgh F, Mestdagh P, Vandesompele J, Menten B, De Preter K, Studer L, Heindryckx B, Durinck K, Roberts S, Speleman F. Recurrent chromosomal imbalances provide selective advantage to human embryonic stem cells under enhanced replicative stress conditions. Genes Chromosomes Cancer 2021; 60:272-281. [PMID: 33336840 DOI: 10.1002/gcc.22931] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 11/07/2022] Open
Abstract
Human embryonic stem cells (hESCs) and embryonal tumors share a number of common features, including a compromised G1/S checkpoint. Consequently, these rapidly dividing hESCs and cancer cells undergo elevated levels of replicative stress, inducing genomic instability that drives chromosomal imbalances. In this context, it is of interest that long-term in vitro cultured hESCs exhibit a remarkable high incidence of segmental DNA copy number gains, some of which are also highly recurrent in certain malignancies such as 17q gain (17q+). The selective advantage of DNA copy number changes in these cells has been attributed to several underlying processes including enhanced proliferation. We hypothesized that these recurrent chromosomal imbalances become rapidly embedded in the cultured hESCs through a replicative stress driven Darwinian selection process. To this end, we compared the effect of hydroxyurea-induced replicative stress vs normal growth conditions in an equally mixed cell population of isogenic euploid and 17q + hESCs. We could show that 17q + hESCs rapidly overtook normal hESCs. Our data suggest that recurrent chromosomal segmental gains provide a proliferative advantage to hESCs under increased replicative stress, a process that may also explain the highly recurrent nature of certain imbalances in cancer.
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Affiliation(s)
- Liselot M Mus
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Stéphane Van Haver
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Mina Popovic
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium
| | - Wim Trypsteen
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Steve Lefever
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Nadja Zeltner
- Center for Molecular Medicine, Department of Biochemistry & Molecular Biology and Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
| | - Yudelca Ogando
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Eva Z Jacobs
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Geertrui Denecker
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Ellen Sanders
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Christophe Van Neste
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Suzanne Vanhauwaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Bieke Decaesteker
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Dieter Deforce
- Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Pieter Mestdagh
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Jo Vandesompele
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Björn Menten
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Katleen De Preter
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Lorenz Studer
- The Center for Stem Cell Biology, Sloan Kettering Institute, New York, USA
- Developmental Biology Program, Sloan Kettering Institute, New York, USA
| | - Björn Heindryckx
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium
| | - Kaat Durinck
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Stephen Roberts
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Frank Speleman
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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13
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Toro A, Anselmino N, Solari C, Francia M, Oses C, Sanchis P, Bizzotto J, Vazquez Echegaray C, Petrone MV, Levi V, Vazquez E, Guberman A. Novel Interplay between p53 and HO-1 in Embryonic Stem Cells. Cells 2020; 10:cells10010035. [PMID: 33383653 PMCID: PMC7823265 DOI: 10.3390/cells10010035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/22/2020] [Accepted: 12/24/2020] [Indexed: 02/06/2023] Open
Abstract
Stem cells genome safeguarding requires strict oxidative stress control. Heme oxygenase-1 (HO-1) and p53 are relevant components of the cellular defense system. p53 controls cellular response to multiple types of harmful stimulus, including oxidative stress. Otherwise, besides having a protective role, HO-1 is also involved in embryo development and in embryonic stem (ES) cells differentiation. Although both proteins have been extensively studied, little is known about their relationship in stem cells. The aim of this work is to explore HO-1-p53 interplay in ES cells. We studied HO-1 expression in p53 knockout (KO) ES cells and we found that they have higher HO-1 protein levels but similar HO-1 mRNA levels than the wild type (WT) ES cell line. Furthermore, cycloheximide treatment increased HO-1 abundance in p53 KO cells suggesting that p53 modulates HO-1 protein stability. Notably, H2O2 treatment did not induce HO-1 expression in p53 KO ES cells. Finally, SOD2 protein levels are also increased while Sod2 transcripts are not in KO cells, further suggesting that the p53 null phenotype is associated with a reinforcement of the antioxidant machinery. Our results demonstrate the existence of a connection between p53 and HO-1 in ES cells, highlighting the relationship between these stress defense pathways.
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Affiliation(s)
- Ayelén Toro
- CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina; (A.T.); (N.A.); (C.S.); (M.F.); (C.O.); (P.S.); (J.B.); (C.V.E.); (M.V.P.); (V.L.)
| | - Nicolás Anselmino
- CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina; (A.T.); (N.A.); (C.S.); (M.F.); (C.O.); (P.S.); (J.B.); (C.V.E.); (M.V.P.); (V.L.)
| | - Claudia Solari
- CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina; (A.T.); (N.A.); (C.S.); (M.F.); (C.O.); (P.S.); (J.B.); (C.V.E.); (M.V.P.); (V.L.)
| | - Marcos Francia
- CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina; (A.T.); (N.A.); (C.S.); (M.F.); (C.O.); (P.S.); (J.B.); (C.V.E.); (M.V.P.); (V.L.)
| | - Camila Oses
- CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina; (A.T.); (N.A.); (C.S.); (M.F.); (C.O.); (P.S.); (J.B.); (C.V.E.); (M.V.P.); (V.L.)
| | - Pablo Sanchis
- CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina; (A.T.); (N.A.); (C.S.); (M.F.); (C.O.); (P.S.); (J.B.); (C.V.E.); (M.V.P.); (V.L.)
| | - Juan Bizzotto
- CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina; (A.T.); (N.A.); (C.S.); (M.F.); (C.O.); (P.S.); (J.B.); (C.V.E.); (M.V.P.); (V.L.)
| | - Camila Vazquez Echegaray
- CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina; (A.T.); (N.A.); (C.S.); (M.F.); (C.O.); (P.S.); (J.B.); (C.V.E.); (M.V.P.); (V.L.)
| | - María Victoria Petrone
- CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina; (A.T.); (N.A.); (C.S.); (M.F.); (C.O.); (P.S.); (J.B.); (C.V.E.); (M.V.P.); (V.L.)
| | - Valeria Levi
- CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina; (A.T.); (N.A.); (C.S.); (M.F.); (C.O.); (P.S.); (J.B.); (C.V.E.); (M.V.P.); (V.L.)
| | - Elba Vazquez
- CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina; (A.T.); (N.A.); (C.S.); (M.F.); (C.O.); (P.S.); (J.B.); (C.V.E.); (M.V.P.); (V.L.)
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Correspondence: (E.V.); (A.G.); Tel.: +54-91144087796 (E.V.); +54-115-285-8683 (A.G.)
| | - Alejandra Guberman
- CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina; (A.T.); (N.A.); (C.S.); (M.F.); (C.O.); (P.S.); (J.B.); (C.V.E.); (M.V.P.); (V.L.)
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Correspondence: (E.V.); (A.G.); Tel.: +54-91144087796 (E.V.); +54-115-285-8683 (A.G.)
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14
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Cruvinel E, Ogusuku I, Cerioni R, Rodrigues S, Gonçalves J, Góes ME, Alvim JM, Silva AC, Lino VDS, Boccardo E, Goulart E, Pereira A, Dariolli R, Valadares M, Biagi D. Long-term single-cell passaging of human iPSC fully supports pluripotency and high-efficient trilineage differentiation capacity. SAGE Open Med 2020; 8:2050312120966456. [PMID: 33149912 PMCID: PMC7586033 DOI: 10.1177/2050312120966456] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/24/2020] [Indexed: 12/11/2022] Open
Abstract
Objectives: To establish a straightforward single-cell passaging cultivation method that enables high-quality maintenance of human induced pluripotent stem cells without the appearance of karyotypic abnormalities or loss of pluripotency. Methods: Cells were kept in culture for over 50 passages, following a structured chronogram of passage and monitoring cell growth by population doubling time calculation and cell confluence. Standard procedures for human induced pluripotent stem cells monitoring as embryonic body formation, karyotyping and pluripotency markers expression were evaluated in order to assess the cellular state in long-term culture. Cells that underwent these tests were then subjected to differentiation into keratinocytes, cardiomyocytes and definitive endoderm to evaluate its differentiation capacity. Results: Human induced pluripotent stem cells clones maintained its pluripotent capability as well as chromosomal integrity and were able to generate derivatives from the three germ layers at high passages by embryoid body formation and high-efficient direct differentiation into keratinocytes, cardiomyocytes and definitive endoderm. Conclusions: Our findings support the routine of human induced pluripotent stem cells single-cell passaging as a reliable procedure even after long-term cultivation, providing healthy human induced pluripotent stem cells to be used in drug discovery, toxicity, and disease modeling as well as for therapeutic approaches.
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Affiliation(s)
| | | | | | | | | | - Maria Elisa Góes
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | | | | | - Vanesca de Souza Lino
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Enrique Boccardo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Ernesto Goulart
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Alexandre Pereira
- Heart Institute (InCor), University of São Paulo Medical School, São Paulo, Brazil
| | - Rafael Dariolli
- PluriCell Biotech, São Paulo, Brazil.,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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15
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Stavish D, Böiers C, Price C, Frith TJR, Halliwell J, Saldaña-Guerrero I, Wray J, Brown J, Carr J, James C, Barbaric I, Andrews PW, Enver T. Generation and trapping of a mesoderm biased state of human pluripotency. Nat Commun 2020; 11:4989. [PMID: 33020476 PMCID: PMC7536399 DOI: 10.1038/s41467-020-18727-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 09/10/2020] [Indexed: 12/22/2022] Open
Abstract
We postulate that exit from pluripotency involves intermediates that retain pluripotency while simultaneously exhibiting lineage-bias. Using a MIXL1 reporter, we explore mesoderm lineage-bias within the human pluripotent stem cell compartment. We identify a substate, which at the single cell level coexpresses pluripotent and mesodermal gene expression programmes. Functionally these cells initiate stem cell cultures and exhibit mesodermal bias in differentiation assays. By promoting mesodermal identity through manipulation of WNT signalling while preventing exit from pluripotency using lysophosphatidic acid, we 'trap' and maintain cells in a lineage-biased stem cell state through multiple passages. These cells correspond to a normal state on the differentiation trajectory, the plasticity of which is evidenced by their reacquisition of an unbiased state upon removal of differentiation cues. The use of 'cross-antagonistic' signalling to trap pluripotent stem cell intermediates with different lineage-bias may have general applicability in the efficient production of cells for regenerative medicine.
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Affiliation(s)
- Dylan Stavish
- The Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
| | - Charlotta Böiers
- Stem Cell Laboratory, Department of Cancer Biology, University College London Cancer Institute, 72 Huntley St, London, WC1E 6AG, UK
| | - Christopher Price
- The Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Thomas J R Frith
- The Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Jason Halliwell
- The Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Ingrid Saldaña-Guerrero
- The Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Jason Wray
- Stem Cell Laboratory, Department of Cancer Biology, University College London Cancer Institute, 72 Huntley St, London, WC1E 6AG, UK
| | - John Brown
- Stem Cell Laboratory, Department of Cancer Biology, University College London Cancer Institute, 72 Huntley St, London, WC1E 6AG, UK
| | - Jonathon Carr
- The Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Chela James
- Stem Cell Laboratory, Department of Cancer Biology, University College London Cancer Institute, 72 Huntley St, London, WC1E 6AG, UK
| | - Ivana Barbaric
- The Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Peter W Andrews
- The Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
| | - Tariq Enver
- Stem Cell Laboratory, Department of Cancer Biology, University College London Cancer Institute, 72 Huntley St, London, WC1E 6AG, UK
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16
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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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17
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Functions of paralogous RNA polymerase III subunits POLR3G and POLR3GL in mouse development. Proc Natl Acad Sci U S A 2020; 117:15702-15711. [PMID: 32576691 DOI: 10.1073/pnas.1922821117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Mammalian cells contain two isoforms of RNA polymerase III (Pol III) that differ in only a single subunit, with POLR3G in one form (Pol IIIα) and the related POLR3GL in the other form (Pol IIIβ). Previous research indicates that POLR3G and POLR3GL are differentially expressed, with POLR3G expression being highly enriched in embryonic stem cells (ESCs) and tumor cells relative to the ubiquitously expressed POLR3GL. To date, the functional differences between these two subunits remain largely unexplored, especially in vivo. Here, we show that POLR3G and POLR3GL containing Pol III complexes bind the same target genes and assume the same functions both in vitro and in vivo and, to a significant degree, can compensate for each other in vivo. Notably, an observed defect in the differentiation ability of POLR3G knockout ESCs can be rescued by exogenous expression of POLR3GL. Moreover, whereas POLR3G knockout mice die at a very early embryonic stage, POLR3GL knockout mice complete embryonic development without noticeable defects but die at about 3 wk after birth with signs of both general growth defects and potential cerebellum-related neuronal defects. The different phenotypes of the knockout mice likely reflect differential expression levels of POLR3G and POLR3GL across developmental stages and between tissues and insufficient amounts of total Pol III in vivo.
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18
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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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19
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Development of genetic quality tests for good manufacturing practice-compliant induced pluripotent stem cells and their derivatives. Sci Rep 2020; 10:3939. [PMID: 32127560 PMCID: PMC7054319 DOI: 10.1038/s41598-020-60466-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 02/05/2020] [Indexed: 02/06/2023] Open
Abstract
Although human induced pluripotent stem cell (hiPSC) lines are karyotypically normal, they retain the potential for mutation in the genome. Accordingly, intensive and relevant quality controls for clinical-grade hiPSCs remain imperative. As a conceptual approach, we performed RNA-seq-based broad-range genetic quality tests on GMP-compliant human leucocyte antigen (HLA)-homozygous hiPSCs and their derivatives under postdistribution conditions to investigate whether sequencing data could provide a basis for future quality control. We found differences in the degree of single-nucleotide polymorphism (SNP) occurring in cells cultured at three collaborating institutes. However, the cells cultured at each centre showed similar trends, in which more SNPs occurred in late-passage hiPSCs than in early-passage hiPSCs after differentiation. In eSNP karyotyping analysis, none of the predicted copy number variations (CNVs) were identified, which confirmed the results of SNP chip-based CNV analysis. HLA genotyping analysis revealed that each cell line was homozygous for HLA-A, HLA-B, and DRB1 and heterozygous for HLA-DPB type. Gene expression profiling showed a similar differentiation ability of early- and late-passage hiPSCs into cardiomyocyte-like, hepatic-like, and neuronal cell types. However, time-course analysis identified five clusters showing different patterns of gene expression, which were mainly related to the immune response. In conclusion, RNA-seq analysis appears to offer an informative genetic quality testing approach for such cell types and allows the early screening of candidate hiPSC seed stocks for clinical use by facilitating safety and potential risk evaluation.
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20
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Goodwin J, Laslett AL, Rugg-Gunn PJ. The application of cell surface markers to demarcate distinct human pluripotent states. Exp Cell Res 2020; 387:111749. [PMID: 31790696 PMCID: PMC6983944 DOI: 10.1016/j.yexcr.2019.111749] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/17/2019] [Accepted: 11/27/2019] [Indexed: 01/24/2023]
Abstract
Recent advances in human pluripotent stem cell (hPSC) research have uncovered different subpopulations within stem cell cultures and have captured a range of pluripotent states that hold distinct molecular and functional properties. At the two ends of the pluripotency spectrum are naïve and primed hPSC, whereby naïve hPSC grown in stringent conditions recapitulate features of the preimplantation human embryo, and the conventionally grown primed hPSC align closer to the early postimplantation embryo. Investigating these cell types will help to define the mechanisms that control early development and should provide new insights into stem cell properties such as cell identity, differentiation and reprogramming. Monitoring cell surface marker expression provides a valuable approach to resolve complex cell populations, to directly compare between cell types, and to isolate viable cells for functional experiments. This review discusses the discovery and applications of cell surface markers to study human pluripotent cell types with a particular focus on the transitions between naïve and primed states. Highlighted areas for future study include the potential functions for the identified cell surface proteins in pluripotency, the production of new high-quality monoclonal antibodies to naïve-specific protein epitopes and the use of cell surface markers to characterise subpopulations within pluripotent states.
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Affiliation(s)
- Jacob Goodwin
- CSIRO Manufacturing, Research Way, Clayton, VIC 3168, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia.
| | - Andrew L Laslett
- CSIRO Manufacturing, Research Way, Clayton, VIC 3168, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia.
| | - Peter J Rugg-Gunn
- Epigenetics Programme, The Babraham Institute, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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21
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Kim MH, Kino-Oka M. Bioengineering Considerations for a Nurturing Way to Enhance Scalable Expansion of Human Pluripotent Stem Cells. Biotechnol J 2020; 15:e1900314. [PMID: 31904180 DOI: 10.1002/biot.201900314] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 11/11/2019] [Indexed: 12/13/2022]
Abstract
Understanding how defects in mechanotransduction affect cell-to-cell variability will add to the fundamental knowledge of human pluripotent stem cell (hPSC) culture, and may suggest new approaches for achieving a robust, reproducible, and scalable process that result in consistent product quality and yields. Here, the current state of the understanding of the fundamental mechanisms that govern the growth kinetics of hPSCs between static and dynamic cultures is reviewed, the factors causing fluctuations are identified, and culture strategies that might eliminate or minimize the occurrence of cell-to-cell variability arising from these fluctuations are discussed. The existing challenges in the development of hPSC expansion methods for enabling the transition from process development to large-scale production are addressed, a mandatory step for industrial and clinical applications of hPSCs.
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Affiliation(s)
- Mee-Hae Kim
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, 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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22
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Petrie JL, Swan C, Ingram RM, Frame FM, Collins AT, Dumay-Odelot H, Teichmann M, Maitland NJ, White RJ. Effects on prostate cancer cells of targeting RNA polymerase III. Nucleic Acids Res 2019; 47:3937-3956. [PMID: 30820548 PMCID: PMC6486637 DOI: 10.1093/nar/gkz128] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/13/2019] [Accepted: 02/19/2019] [Indexed: 12/12/2022] Open
Abstract
RNA polymerase (pol) III occurs in two forms, containing either the POLR3G subunit or the related paralogue POLR3GL. Whereas POLR3GL is ubiquitous, POLR3G is enriched in undifferentiated cells. Depletion of POLR3G selectively triggers proliferative arrest and differentiation of prostate cancer cells, responses not elicited when POLR3GL is depleted. A small molecule pol III inhibitor can cause POLR3G depletion, induce similar differentiation and suppress proliferation and viability of cancer cells. This response involves control of the fate-determining factor NANOG by small RNAs derived from Alu short interspersed nuclear elements. Tumour initiating activity in vivo can be reduced by transient exposure to the pol III inhibitor. Untransformed prostate cells appear less sensitive than cancer cells to pol III depletion or inhibition, raising the possibility of a therapeutic window.
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Affiliation(s)
- John L Petrie
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Caroline Swan
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Richard M Ingram
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Fiona M Frame
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Anne T Collins
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Hélène Dumay-Odelot
- Université de Bordeaux, ARNA Laboratory, F-33076 Bordeaux, France INSERM, U1212 - CNRS UMR 5320, ARNA Laboratory, F-33000 Bordeaux, France
| | - Martin Teichmann
- Université de Bordeaux, ARNA Laboratory, F-33076 Bordeaux, France INSERM, U1212 - CNRS UMR 5320, ARNA Laboratory, F-33000 Bordeaux, France
| | - Norman J Maitland
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Robert J White
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
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23
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Liu LP, Zheng YW. Predicting differentiation potential of human pluripotent stem cells: Possibilities and challenges. World J Stem Cells 2019; 11:375-382. [PMID: 31396366 PMCID: PMC6682503 DOI: 10.4252/wjsc.v11.i7.375] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/12/2019] [Accepted: 06/20/2019] [Indexed: 02/06/2023] Open
Abstract
The capability of human pluripotent stem cell (hPSC) lines to propagate indefinitely and differentiate into derivatives of three embryonic germ layers makes these cells be powerful tools for basic scientific research and promising agents for translational medicine. However, variations in differentiation tendency and efficiency as well as pluripotency maintenance necessitate the selection of hPSC lines for the intended applications to save time and cost. To screen the qualified cell lines and exclude problematic cell lines, their pluripotency must be confirmed initially by traditional methods such as teratoma formation or by high-throughput gene expression profiling assay. Additionally, their differentiation potential, particularly the lineage-specific differentiation propensities of hPSC lines, should be predicted in an early stage. As a complement to the teratoma assay, RNA sequencing data provide a quantitative estimate of the differentiation ability of hPSCs in vivo. Moreover, multiple scorecards have been developed based on selected gene sets for predicting the differentiation potential into three germ layers or the desired cell type many days before terminal differentiation. For clinical application of hPSCs, the malignant potential of the cells must also be evaluated. A combination of histologic examination of teratoma with quantitation of gene expression data derived from teratoma tissue provides safety-related predictive information by detecting immature teratomas, malignancy marker expression, and other parameters. Although various prediction methods are available, distinct limitations remain such as the discordance of results between different assays and requirement of a long time and high labor and cost, restricting their wide applications in routine studies. Therefore, simpler and more rapid detection assays with high specificity and sensitivity that can be used to monitor the status of hPSCs at any time and fewer targeted markers that are more specific for a given desired cell type are urgently needed.
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Affiliation(s)
- Li-Ping Liu
- Institute of Regenerative Medicine, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang 212001, Jiangsu Province, China
- University of Tsukuba Faculty of Medicine, Tsukuba, Ibaraki 305-8575, Japan
| | - Yun-Wen Zheng
- Institute of Regenerative Medicine, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang 212001, Jiangsu Province, China
- University of Tsukuba Faculty of Medicine, Tsukuba, Ibaraki 305-8575, Japan
- Yokohama City University School of Medicine, Yokohama 236-0004, Japan
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24
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Colicino EG, Stevens K, Curtis E, Rathbun L, Bates M, Manikas J, Amack J, Freshour J, Hehnly H. Chromosome misalignment is associated with PLK1 activity at cenexin-positive mitotic centrosomes. Mol Biol Cell 2019; 30:1598-1609. [PMID: 31042116 PMCID: PMC6727634 DOI: 10.1091/mbc.e18-12-0817] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 03/28/2019] [Accepted: 04/25/2019] [Indexed: 02/02/2023] Open
Abstract
The mitotic kinase, polo-like kinase 1 (PLK1), facilitates the assembly of the two mitotic spindle poles, which are required for the formation of the microtubule-based spindle that ensures appropriate chromosome distribution into the two forming daughter cells. Spindle poles are asymmetric in composition. One spindle pole contains the oldest mitotic centriole, the mother centriole, where the majority of cenexin, the mother centriole appendage protein and PLK1 binding partner, resides. We hypothesized that PLK1 activity is greater at the cenexin-positive older spindle pole. Our studies found that PLK1 asymmetrically localizes between spindle poles under conditions of chromosome misalignment, and chromosomes tend to misalign toward the oldest spindle pole in a cenexin- and PLK1-dependent manner. During chromosome misalignment, PLK1 activity is increased specifically at the oldest spindle pole, and this increase in activity is lost in cenexin-depleted cells. We propose a model where PLK1 activity elevates in response to misaligned chromosomes at the oldest spindle pole during metaphase.
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Affiliation(s)
- Erica G. Colicino
- Biology Department, Syracuse University, Syracuse, NY 13210
- Department of Cell and Developmental Biology, Upstate Medical University, Syracuse, NY 13210
| | | | - Erin Curtis
- Biology Department, Syracuse University, Syracuse, NY 13210
| | | | - Michael Bates
- Biology Department, Syracuse University, Syracuse, NY 13210
| | - Julie Manikas
- Biology Department, Syracuse University, Syracuse, NY 13210
| | - Jeffrey Amack
- Department of Cell and Developmental Biology, Upstate Medical University, Syracuse, NY 13210
| | - Judy Freshour
- Biology Department, Syracuse University, Syracuse, NY 13210
| | - Heidi Hehnly
- Biology Department, Syracuse University, Syracuse, NY 13210
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25
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MacArthur CC, Pradhan S, Wetton N, Zarrabi A, Dargitz C, Sridharan M, Jackson S, Pickle L, Lakshmipathy U. Generation and comprehensive characterization of induced pluripotent stem cells for translational research. Regen Med 2019; 14:505-524. [PMID: 31115261 DOI: 10.2217/rme-2018-0148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) hold immense potential in disease modeling, drug discovery and regenerative medicine. Despite advances in reprogramming methods, generation of clinical-grade iPSCs remains a challenge. Reported here is the first off-the-shelf reprogramming kit, CTS CytoTune-iPS 2.1, specifically designed for clinical and translational research. Workflow gaps were identified, and methods developed were used to consistently generate iPSC from multiple cell types. Resulting clones were subjected to characterization that included confirmation of pluripotency, preservation of genomic integrity and authentication of cell banks via an array of molecular methods including high resolution microarray and next-generation sequencing. Development of integrated xeno-free workflows combined with comprehensive characterization offers generation of high-quality iPSCs that are suited for clinical and translational research.
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Affiliation(s)
- Chad C MacArthur
- Cell Biology, Life Sciences Solutions, Thermo Fisher Scientific, Carlsbad, CA 92008, USA
| | - Suman Pradhan
- Cell Biology, Life Sciences Solutions, Thermo Fisher Scientific, Carlsbad, CA 92008, USA
| | - Nichole Wetton
- Cell Biology, Life Sciences Solutions, Thermo Fisher Scientific, Carlsbad, CA 92008, USA
| | - Aryan Zarrabi
- Cell Biology, Life Sciences Solutions, Thermo Fisher Scientific, Carlsbad, CA 92008, USA
| | - Carl Dargitz
- Cell Biology, Life Sciences Solutions, Thermo Fisher Scientific, Carlsbad, CA 92008, USA
| | - Mahalakshmi Sridharan
- Cell Biology, Life Sciences Solutions, Thermo Fisher Scientific, Carlsbad, CA 92008, USA
| | - Stephen Jackson
- Cell Biology, Life Sciences Solutions, Thermo Fisher Scientific, Carlsbad, CA 92008, USA
| | - Loni Pickle
- Cell Biology, Life Sciences Solutions, Thermo Fisher Scientific, Carlsbad, CA 92008, USA
| | - Uma Lakshmipathy
- Cell Biology, Life Sciences Solutions, Thermo Fisher Scientific, Carlsbad, CA 92008, USA
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26
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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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27
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Analysis of the Paternally-Imprinted DLK1-MEG3 and IGF2-H19 Tandem Gene Loci in NT2 Embryonal Carcinoma Cells Identifies DLK1 as a Potential Therapeutic Target. Stem Cell Rev Rep 2019; 14:823-836. [PMID: 29980981 DOI: 10.1007/s12015-018-9838-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The paternally-imprinted genes insulin-like growth factor 2 (IGF2), H19, delta-like homologue 1 (DLK1), and maternally-expressed gene 3 (MEG3) are expressed from the tandem gene loci IGF2-H19 and DLK1-MEG3, which play crucial roles in initiating embryogenesis and development. The erasure of imprinting (EOI) at differentially methylated regions (DMRs) which regulate the expression of these genes maintains the developmental quiescence of primordial germ cells (PGCs) migrating through the embryo proper during embryogenesis and prevents them from forming teratomas. To address the potential involvement of the IGF2-H19 and DLK1-MEG3 loci in the pathogenesis of embryonal carcinoma (EC), we investigated their genomic imprinting at DMRs in the human PGC-derived EC cell line NTera-2 (NT2). We observed EOI at the IGF2-H19 locus and, somewhat to our surprise, a loss of imprinting (LOI) at the DLK1-MEG3 locus. As a result, NT2 cells express imprinted gene ratios from these loci such that there are i) low levels of the proliferation-promoting IGF2 relative to ii) high levels of the proliferation-inhibiting long noncoding RNA (lncRNA) H19 and iii) high levels of proliferation-promoting DLK1 relative to iv) low levels of the proliferation-inhibiting lncRNA MEG3. Consistent with this pattern of expression, the knockdown of DLK1 mRNA by shRNA resulted in decreased in vitro cell proliferation and in vivo tumor growth as well as decreased in vivo organ seeding by NT2 cells. Furthermore, treatment of NT2 cells with the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine (5-azaD) inhibited their proliferation. This inhibition was accompanied by changes in expression of both tandem gene sets: a decrease in the expression of DLK1 and upregulation of the proliferation-inhibiting lncRNA MEG3, and at the same time upregulation of IGF2 and downregulation of the lncRNA H19. These results suggest that the DLK1-MEG3 locus, and not the IGF2-H19 locus, drives the tumorigenicity of NT2 cells. Based on these results, we identified DLK1 as a novel treatment target for EC that could be downregulated by 5-azaD.
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28
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Henry MP, Hawkins JR, Boyle J, Bridger JM. The Genomic Health of Human Pluripotent Stem Cells: Genomic Instability and the Consequences on Nuclear Organization. Front Genet 2019; 9:623. [PMID: 30719030 PMCID: PMC6348275 DOI: 10.3389/fgene.2018.00623] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/23/2018] [Indexed: 12/11/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) are increasingly used for cell-based regenerative therapies worldwide, with embryonic and induced pluripotent stem cells as potential treatments for debilitating and chronic conditions, such as age-related macular degeneration, Parkinson's disease, spinal cord injuries, and type 1 diabetes. However, with the level of genomic anomalies stem cells generate in culture, their safety may be in question. Specifically, hPSCs frequently acquire chromosomal abnormalities, often with gains or losses of whole chromosomes. This review discusses how important it is to efficiently and sensitively detect hPSC aneuploidies, to understand how these aneuploidies arise, consider the consequences for the cell, and indeed the individual to whom aneuploid cells may be administered.
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Affiliation(s)
- Marianne P Henry
- Advanced Therapies Division, National Institute for Biological Standards and Control, Potters Bar, United Kingdom.,Laboratory of Nuclear and Genomic Health, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, United Kingdom
| | - J Ross Hawkins
- Advanced Therapies Division, National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | - Jennifer Boyle
- Advanced Therapies Division, National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | - Joanna M Bridger
- Laboratory of Nuclear and Genomic Health, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, United Kingdom
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29
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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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30
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Shilina MA, Grinchuk TM, Anatskaya OV, Vinogradov AE, Alekseenko LL, Elmuratov AU, Nikolsky NN. Cytogenetic and Transcriptomic Analysis of Human Endometrial MSC Retaining Proliferative Activity after Sublethal Heat Shock. Cells 2018; 7:cells7110184. [PMID: 30366433 PMCID: PMC6262560 DOI: 10.3390/cells7110184] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/19/2018] [Accepted: 10/23/2018] [Indexed: 12/14/2022] Open
Abstract
Temperature is an important exogenous factor capable of leading to irreversible processes in the vital activity of cells. However, the long-term effects of heat shock (HS) on mesenchymal stromal cells (MSC) remain unstudied. We investigated the karyotype and DNA repair drivers and pathways in the human endometrium MSC (eMSC) survived progeny at passage 6 after sublethal heat stress (sublethal heat stress survived progeny (SHS-SP)). G-banding revealed an outbreak of random karyotype instability caused by chromosome breakages and aneuploidy. Molecular karyotyping confirmed the random nature of this instability. Transcriptome analysis found homologous recombination (HR) deficiency that most likely originated from the low thermostability of the AT-rich HR driving genes. SHS-SP protection from transformation is provided presumably by low oncogene expression maintained by tight co-regulation between thermosensitive HR drivers BRCA, ATM, ATR, and RAD51 (decreasing expression after SHS), and oncogenes mTOR, MDM2, KRAS, and EGFR. The cancer-related transcriptomic features previously identified in hTERT transformed MSC in culture were not found in SHS-SP, suggesting no traits of malignancy in them. The entrance of SHS-SP into replicative senescence after 25 passages confirms their mortality and absence of transformation features. Overall, our data indicate that SHS may trigger non-tumorigenic karyotypic instability due to HR deficiency and decrease of oncogene expression in progeny of SHS-survived MSC. These data can be helpful for the development of new therapeutic approaches in personalized medicine.
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Affiliation(s)
- Mariia A Shilina
- Institute of Cytology, Russian Academy of Sciences, Tikhoretskay Ave 4, St. 194064 Petersburg, Russia.
| | - Tatiana M Grinchuk
- Institute of Cytology, Russian Academy of Sciences, Tikhoretskay Ave 4, St. 194064 Petersburg, Russia.
| | - Olga V Anatskaya
- Institute of Cytology, Russian Academy of Sciences, Tikhoretskay Ave 4, St. 194064 Petersburg, Russia.
| | - Alexander E Vinogradov
- Institute of Cytology, Russian Academy of Sciences, Tikhoretskay Ave 4, St. 194064 Petersburg, Russia.
| | - Larisa L Alekseenko
- Institute of Cytology, Russian Academy of Sciences, Tikhoretskay Ave 4, St. 194064 Petersburg, Russia.
| | - Artem U Elmuratov
- Institute of Biomedical Chemistry (IBMC) of Russian Academy of Sciences, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia.
- Medical Genetics Centre Genotek, Nastavnichesky Alley 17-1-15, 10510 Moscow, Russia.
| | - Nikolai N Nikolsky
- Institute of Cytology, Russian Academy of Sciences, Tikhoretskay Ave 4, St. 194064 Petersburg, Russia.
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31
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Chen CY, Lanz RB, Walkey CJ, Chang WH, Lu W, Johnson DL. Maf1 and Repression of RNA Polymerase III-Mediated Transcription Drive Adipocyte Differentiation. Cell Rep 2018; 24:1852-1864. [PMID: 30110641 PMCID: PMC6138453 DOI: 10.1016/j.celrep.2018.07.046] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 04/05/2018] [Accepted: 07/12/2018] [Indexed: 12/11/2022] Open
Abstract
RNA polymerase (pol) III transcribes a variety of small untranslated RNAs involved in transcription, RNA processing, and translation. RNA pol III and its components are altered in various human developmental disorders, yet their roles in cell fate determination and development are poorly understood. Here we demonstrate that Maf1, a transcriptional repressor, promotes induction of mouse embryonic stem cells (mESCs) into mesoderm. Reduced Maf1 expression in mESCs and preadipocytes impairs adipogenesis, while ectopic Maf1 expression in Maf1-deficient cells enhances differentiation. RNA pol III repression by chemical inhibition or knockdown of Brf1 promotes adipogenesis. Altered RNA pol III-dependent transcription produces select changes in mRNAs with a significant enrichment of adipogenic gene signatures. Furthermore, RNA pol III-mediated transcription positively regulates long non-coding RNA H19 and Wnt6 expression, established adipogenesis inhibitors. Together, these studies reveal an important and unexpected function for RNA pol III-mediated transcription and Maf1 in mesoderm induction and adipocyte differentiation.
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Affiliation(s)
- Chun-Yuan Chen
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA, USA; Department of Molecular and Cellular Biology and the Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Rainer B Lanz
- Department of Molecular and Cellular Biology and the Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Christopher J Walkey
- Department of Molecular and Cellular Biology and the Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Wen-Hsuan Chang
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | - Wange Lu
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA, USA; Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, USA
| | - Deborah L Johnson
- Department of Molecular and Cellular Biology and the Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.
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32
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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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Fan JR, Lee HT, Lee W, Lin CH, Hsu CY, Hsieh CH, Shyu WC. Potential role of CBX7 in regulating pluripotency of adult human pluripotent-like olfactory stem cells in stroke model. Cell Death Dis 2018; 9:502. [PMID: 29717132 PMCID: PMC5931587 DOI: 10.1038/s41419-018-0519-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 03/08/2018] [Accepted: 03/12/2018] [Indexed: 12/17/2022]
Abstract
The adult olfactory mucosa, a highly regenerative tissue with unique life-long neurogenesis ability, is thought to harbor a naïve yet tightly controlled stem cell population. It will provide unique benefits in various stem cell-based therapies, such as stroke treatment. Here, we identified a subpopulation of adult pluripotent-like olfactory stem cells (APOSCs), which were modulated by an epigenetic repressor of CBX7. APOSCs form a floating sphere, express pluripotency markers Nanog, Oct-4, Sox-2, and SSEA-4 and show alkaline phosphatase activity. In addition, APOSCs display self-renewal and a pluripotent potential to differentiate into all three germ layers. Moreover, APOSCs coexpress pluripotency markers with CBX7. Within their natural niche, APOSCs from CBX7+/+ mice responded promptly to either spontaneous or injury-induced tissue regeneration. However, APOSCs from CBX7−/− mice manifested an impaired self-renewal and differentiation potential. Similarly, in vitro-cultivated CBX7−/− APOSCs underwent premature senescence, whereas CBX7+/+ APOSCs still actively divided, indicating that CBX7 is required for the self-renewal of APOSCs. Intracerebral implantation of APOSCs improved the stroke-mediated neurological dysfunction in rodents. These findings indicate that CBX7 plays a critical role in the regenerative properties of APOSCs and indicate the safety and feasibility of implantation of autologous APOSCs in stroke treatment.
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Affiliation(s)
- Jia-Rong Fan
- Translational Medicine Research Center, and Department of Neurology, China Medical University Hospital, Taichung, 40440, Taiwan
| | - Hsu-Tung Lee
- Department of Neurosurgery, Taichung Veterans General Hospital, Taichung, 40421, Taiwan.,Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Wei Lee
- Translational Medicine Research Center, and Department of Neurology, China Medical University Hospital, Taichung, 40440, Taiwan
| | - Chen-Huan Lin
- Translational Medicine Research Center, and Department of Neurology, China Medical University Hospital, Taichung, 40440, Taiwan
| | - Chun Y Hsu
- Graduate Institute of Biomedical Science, China Medical University Hospital, Taichung, 40440, Taiwan
| | - Chia-Hung Hsieh
- Graduate Institute of Biomedical Science, China Medical University Hospital, Taichung, 40440, Taiwan.
| | - Woei-Cherng Shyu
- Translational Medicine Research Center, and Department of Neurology, China Medical University Hospital, Taichung, 40440, Taiwan. .,Graduate Institute of Biomedical Science, China Medical University Hospital, Taichung, 40440, Taiwan. .,Department of Occupational Therapy, Asia University, Taichung, Taiwan.
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34
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Clinical application of cell, gene and tissue therapies in Spain. Rev Clin Esp 2018. [DOI: 10.1016/j.rceng.2017.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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35
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Bruter AV, Kandarakov OF, Belyavsky AV. Persistence of plasmid-mediated expression of transgenes in human mesenchymal stem cells depends primarily on CpG levels of both vector and transgene. J Gene Med 2018; 20:e3009. [DOI: 10.1002/jgm.3009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 01/20/2018] [Accepted: 01/20/2018] [Indexed: 01/25/2023] Open
Affiliation(s)
- Alexandra V. Bruter
- Russian Academy of Sciences; Engelhardt Institute of Molecular Biology; Moscow Russia
| | - Oleg F. Kandarakov
- Russian Academy of Sciences; Engelhardt Institute of Molecular Biology; Moscow Russia
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36
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Lund RJ, Rahkonen N, Malonzo M, Kauko L, Emani MR, Kivinen V, Närvä E, Kemppainen E, Laiho A, Skottman H, Hovatta O, Rasool O, Nykter M, Lähdesmäki H, Lahesmaa R. RNA Polymerase III Subunit POLR3G Regulates Specific Subsets of PolyA + and SmallRNA Transcriptomes and Splicing in Human Pluripotent Stem Cells. Stem Cell Reports 2018; 8:1442-1454. [PMID: 28494942 PMCID: PMC5425787 DOI: 10.1016/j.stemcr.2017.04.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 04/13/2017] [Accepted: 04/13/2017] [Indexed: 11/17/2022] Open
Abstract
POLR3G is expressed at high levels in human pluripotent stem cells (hPSCs) and is required for maintenance of stem cell state through mechanisms not known in detail. To explore how POLR3G regulates stem cell state, we carried out deep-sequencing analysis of polyA+ and smallRNA transcriptomes present in hPSCs and regulated in POLR3G-dependent manner. Our data reveal that POLR3G regulates a specific subset of the hPSC transcriptome, including multiple transcript types, such as protein-coding genes, long intervening non-coding RNAs, microRNAs and small nucleolar RNAs, and affects RNA splicing. The primary function of POLR3G is in the maintenance rather than repression of transcription. The majority of POLR3G polyA+ transcriptome is regulated during differentiation, and the key pluripotency factors bind to the promoters of at least 30% of the POLR3G-regulated transcripts. Among the direct targets of POLR3G, POLG is potentially important in sustaining stem cell status in a POLR3G-dependent manner.
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Affiliation(s)
- Riikka J Lund
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland.
| | - Nelly Rahkonen
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Maia Malonzo
- Department of Computer Science, Aalto University, Espoo 02150, Finland
| | - Leni Kauko
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Maheswara Reddy Emani
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Virpi Kivinen
- Faculty of Medicine and Life Sciences, BioMediTech, University of Tampere, Tampere 33014, Finland
| | - Elisa Närvä
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Esko Kemppainen
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Asta Laiho
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Heli Skottman
- Faculty of Medicine and Life Sciences, BioMediTech, University of Tampere, Tampere 33014, Finland
| | - Outi Hovatta
- Department CLINTEC, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm 171 77, Sweden
| | - Omid Rasool
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Matti Nykter
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland; Faculty of Medicine and Life Sciences, BioMediTech, University of Tampere, Tampere 33014, Finland
| | - Harri Lähdesmäki
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland; Department of Computer Science, Aalto University, Espoo 02150, Finland
| | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland
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37
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Selection of Suitable Reference Genes for Quantitative Real-Time PCR Normalization in Human Stem Cell Research. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1119:151-168. [PMID: 30267307 DOI: 10.1007/5584_2018_277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Quantitative real-time polymerase chain reaction (qRT-PCR) is a widely utilized method for evaluating the gene expressions in stem cell research. This method enables researchers to obtain fast and precise results, but the accuracy of the data depends on certain factors, such as those associated with biological sample preparation and PCR efficiency. In order to achieve accurate and reliable results, it is of utmost importance to designate the reference genes, the expressions of which are suitable to all kinds of experimental conditions. Hence it is vital to normalize the qRT-PCR data by using the reference genes. In recent years, it has been found that the expression levels of reference genes widely used in stem cell research present a substantial amount of variation and are not necessarily suitable for normalization. This chapter at hand stresses the significance of selecting suitable reference genes from the point view of human stem cell research.
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38
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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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39
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Peh GSL, Ang HP, Lwin CN, Adnan K, George BL, Seah XY, Lin SJ, Bhogal M, Liu YC, Tan DT, Mehta JS. Regulatory Compliant Tissue-Engineered Human Corneal Endothelial Grafts Restore Corneal Function of Rabbits with Bullous Keratopathy. Sci Rep 2017; 7:14149. [PMID: 29074873 PMCID: PMC5658403 DOI: 10.1038/s41598-017-14723-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 10/16/2017] [Indexed: 01/19/2023] Open
Abstract
Corneal transplantation is the only treatment available to restore vision for individuals with blindness due to corneal endothelial dysfunction. However, severe shortage of available donor corneas remains a global challenge. Functional regulatory compliant tissue-engineered corneal endothelial graft substitute can alleviate this reliance on cadaveric corneal graft material. Here, isolated primary human corneal endothelial cells (CEnCs) propagated using a dual media approach refined towards regulatory compliance showed expression of markers indicative of the human corneal endothelium, and can be tissue-engineered onto thin corneal stromal carriers. Both cellular function and clinical adaptability was demonstrated in a pre-clinical rabbit model of bullous keratopathy using a tissue-engineered endothelial keratoplasty (TE-EK) approach, adapted from routine endothelial keratoplasty procedure for corneal transplantation in human patients. Cornea thickness of rabbits receiving TE-EK graft gradually reduced over the first two weeks, and completely recovered to a thickness of approximately 400 µm by the third week of transplantation, whereas corneas of control rabbits remained significantly thicker over 1,000 µm (p < 0.05) throughout the course of the study. This study showed convincing evidence of the adaptability of the propagated CEnCs and their functionality via a TE-EK approach, which holds great promises in translating the use of cultured CEnCs into the clinic.
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Affiliation(s)
- Gary S L Peh
- Tissue Engineering and Stem Cell Group, Singapore Eye Research Institute, Singapore, Singapore. .,Duke-NUS Graduate Medical School, Singapore, Singapore.
| | - Heng-Pei Ang
- Tissue Engineering and Stem Cell Group, Singapore Eye Research Institute, Singapore, Singapore
| | - Chan N Lwin
- Tissue Engineering and Stem Cell Group, Singapore Eye Research Institute, Singapore, Singapore
| | - Khadijah Adnan
- Tissue Engineering and Stem Cell Group, Singapore Eye Research Institute, Singapore, Singapore
| | - Benjamin L George
- Tissue Engineering and Stem Cell Group, Singapore Eye Research Institute, Singapore, Singapore.,Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Xin-Yi Seah
- Tissue Engineering and Stem Cell Group, Singapore Eye Research Institute, Singapore, Singapore
| | - Shu-Jun Lin
- Tissue Engineering and Stem Cell Group, Singapore Eye Research Institute, Singapore, Singapore
| | - Maninder Bhogal
- Tissue Engineering and Stem Cell Group, Singapore Eye Research Institute, Singapore, Singapore.,Department of Corneal and External Disease, Moorfields Eye Hospital, London, UK
| | - Yu-Chi Liu
- Tissue Engineering and Stem Cell Group, Singapore Eye Research Institute, Singapore, Singapore.,Singapore National Eye Centre, Singapore, Singapore
| | - Donald T Tan
- Tissue Engineering and Stem Cell Group, Singapore Eye Research Institute, Singapore, Singapore.,Singapore National Eye Centre, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jodhbir S Mehta
- Tissue Engineering and Stem Cell Group, Singapore Eye Research Institute, Singapore, Singapore. .,Duke-NUS Graduate Medical School, Singapore, Singapore. .,Singapore National Eye Centre, Singapore, Singapore. .,School of Material Science and Engineering, Nanyang Technological University, Singapore, Singapore.
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40
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Gálvez-Martín P, Ruiz A, Clares B. Clinical application of cell, gene and tissue therapies in Spain. Rev Clin Esp 2017; 218:199-206. [PMID: 29032959 DOI: 10.1016/j.rce.2017.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 07/26/2017] [Accepted: 08/13/2017] [Indexed: 11/30/2022]
Abstract
Scientific and technical advances in the areas of biomedicine and regenerative medicine have enabled the development of new treatments known as "advanced therapies", which encompass cell therapy, genetics and tissue engineering. The biologic products that can be manufactured from these elements are classified from the standpoint of the Spanish Agency of Medication and Health Products in advanced drug therapies, blood products and transplants. This review seeks to provide scientific and administrative information for clinicians on the use of these biologic resources.
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Affiliation(s)
- P Gálvez-Martín
- Departamento de Farmacia y Tecnología Farmacéutica, Facultad de Farmacia, Universidad de Granada, Granada, España.
| | - A Ruiz
- Departamento de Farmacia y Tecnología Farmacéutica, Facultad de Farmacia, Universidad de Granada, Granada, España
| | - B Clares
- Departamento de Farmacia y Tecnología Farmacéutica, Facultad de Farmacia, Universidad de Granada, Granada, España
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41
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Ko DW, Yoon JK, Ahn JI, Lee M, Yang WS, Ahn JY, Lim JM. The importance of post-thaw subculture for standardizing cellular activity of fresh or cryopreserved mouse embryonic stem cells. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2017; 31:335-343. [PMID: 28823125 PMCID: PMC5838338 DOI: 10.5713/ajas.17.0294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 07/08/2017] [Accepted: 08/07/2017] [Indexed: 12/25/2022]
Abstract
Objective Remarkable difference in cellular activity was found between early and late subpassaged embryonic stem cell (ESCs) lines, which can be created by subtle changes in cell manipulation protocol. This study subsequently examined whether post-thaw subculture of early subpassaged ESC lines could further affect the activity of the ESCs. Methods Fresh (as a control treatment) or cryopreserved F1 hybrid (B6CBAF1) early ESC lines (C57BL/6xCBA) of the 4 (P4) or the 19 passage (P19) were subcultured once, twice or six times under the same condition. The post-thaw survival of the ESCs was monitored after the post-treatment subculture and the ability of cell proliferation, reactive oxygen species (ROS) generation, apoptosis and mitochondrial ATP synthesis was subsequently examined. Results Regardless of the subculture number, P19 ESCs showed better (p<0.05) doubling time and less ATP production than P4 ESCs and such difference was not influenced by fresh or cryopreservation. The difference between P4 and P19 ESC lines became decreased as the post-treatment subculture was increased and the six times subculture eliminated such difference. Similarly, transient but prominent difference in ROS production and apoptotic cell number was detected between P4 and P19 ESCs only at the 1st subculture after treatment, but no statistical differences between two ESC lines was detected in other observations. Conclusion The results of this study suggest that post-thaw subculture of ESCs under the same environment is recommended for standardizing their cellular activity. The activity of cell proliferation ability and ATP synthesis can be used as parameters for quality control of ESCs.
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Affiliation(s)
- Dong Woo Ko
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.,Research Institutes of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Jung Ki Yoon
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.,Research Institutes of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Jong Il Ahn
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.,Research Institutes of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Myungook Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.,Research Institutes of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Woo Sub Yang
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.,Research Institutes of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Ji Yeon Ahn
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Jeong Mook Lim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.,Research Institutes of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.,GreenBio Research Institute, Seoul National University, Pyeongchang 25354, Korea
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42
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Picot T, Aanei CM, Fayard A, Flandrin-Gresta P, Tondeur S, Gouttenoire M, Tavernier-Tardy E, Wattel E, Guyotat D, Campos L. Expression of embryonic stem cell markers in acute myeloid leukemia. Tumour Biol 2017; 39:1010428317716629. [PMID: 28718379 DOI: 10.1177/1010428317716629] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Acute myeloid leukemia is driven by leukemic stem cells which can be identified by cross lineage expression or arrest of differentiation compared to normal hematopoietic stem cells. Self-renewal and lack of differentiation are also features of stem cells and have been associated with the expression of embryonic genes. The aim of our study was to evaluate the expression of embryonic antigens (OCT4, NANOG, SOX2, SSEA1, SSEA3) in hematopoietic stem cell subsets (CD34+CD38- and CD34+CD38+) from normal bone marrows and in samples from acute myeloid leukemia patients. We observed an upregulation of the transcription factors OCT4 and SOX2 in leukemic cells as compared to normal cells. Conversely, SSEA1 protein was downregulated in leukemic cells. The expression of OCT4, SOX2, and SSEA3 was higher in CD34+CD38- than in CD34+CD38+ subsets in leukemic cells. There was no correlation with biological characteristics of the leukemia. We evaluated the prognostic value of marker expression in 69 patients who received an intensive treatment. The rate of complete remission was not influenced by the level of expression of markers. Overall survival was significantly better for patients with high SOX2 levels, which was unexpected because of the inverse correlation with favorable genetic subtypes. These results prompt us to evaluate the potential role of these markers in leukemogenesis and to test their relevance for better leukemic stem cell identification.
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Affiliation(s)
- Tiphanie Picot
- 1 Laboratoire d'Hématologie, CHU de Saint-Etienne, Saint-Etienne, France.,2 UMR 5239, Laboratoire de Biologie et Modélisation de la Cellule, Lyon, France
| | - Carmen Mariana Aanei
- 1 Laboratoire d'Hématologie, CHU de Saint-Etienne, Saint-Etienne, France.,2 UMR 5239, Laboratoire de Biologie et Modélisation de la Cellule, Lyon, France
| | - Amandine Fayard
- 3 Département d'Hématologie, Institut de Cancérologie Lucien Neuwirth, Saint-Priest-en-Jarez, France
| | - Pascale Flandrin-Gresta
- 1 Laboratoire d'Hématologie, CHU de Saint-Etienne, Saint-Etienne, France.,2 UMR 5239, Laboratoire de Biologie et Modélisation de la Cellule, Lyon, France
| | - Sylvie Tondeur
- 1 Laboratoire d'Hématologie, CHU de Saint-Etienne, Saint-Etienne, France.,2 UMR 5239, Laboratoire de Biologie et Modélisation de la Cellule, Lyon, France
| | - Marina Gouttenoire
- 3 Département d'Hématologie, Institut de Cancérologie Lucien Neuwirth, Saint-Priest-en-Jarez, France
| | - Emmanuelle Tavernier-Tardy
- 2 UMR 5239, Laboratoire de Biologie et Modélisation de la Cellule, Lyon, France.,3 Département d'Hématologie, Institut de Cancérologie Lucien Neuwirth, Saint-Priest-en-Jarez, France
| | - Eric Wattel
- 2 UMR 5239, Laboratoire de Biologie et Modélisation de la Cellule, Lyon, France
| | - Denis Guyotat
- 2 UMR 5239, Laboratoire de Biologie et Modélisation de la Cellule, Lyon, France.,3 Département d'Hématologie, Institut de Cancérologie Lucien Neuwirth, Saint-Priest-en-Jarez, France
| | - Lydia Campos
- 1 Laboratoire d'Hématologie, CHU de Saint-Etienne, Saint-Etienne, France.,2 UMR 5239, Laboratoire de Biologie et Modélisation de la Cellule, Lyon, France
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43
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Weed LS, Mills JA. Strategies for retinal cell generation from human pluripotent stem cells. Stem Cell Investig 2017; 4:65. [PMID: 28815176 DOI: 10.21037/sci.2017.07.02] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/24/2017] [Indexed: 12/22/2022]
Abstract
Induced pluripotent stem cells (iPSCs) are specialized self-renewing cells that are generated by exogenously expressing pluripotency-associated transcription factors in somatic cells such as fibroblasts, peripheral blood mononuclear cells, or lymphoblastoid cell lines (LCLs). iPSCs are functionally similar to naturally pluripotent embryonic stem cells (ESCs) in their capacity to propagate indefinitely and potential to differentiate into all human cell types, and are devoid of the associated ethical complications of origin. iPSCs are useful for studying embryonic development, disease modeling, and drug screening. Additionally, iPSCs provide a personalized approach for pathological studies, particularly for diseases that lack appropriate animal models. Retinal cell differentiations using iPSCs have been successful in this regard. Several protocols to generate various retinal cells have been developed to maximize a specific cell type or, most recently, to mimic in vivo retinal structure and cellular environment. As differentiation protocols continue to improve we are likely to see an increase in our basic understanding of various retinal degenerative diseases and the utilization of iPSCs in clinical trials.
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Affiliation(s)
- Lindsey S Weed
- Center for Advanced Retinal and Ocular Therapeutics, F.M. Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jason A Mills
- Center for Advanced Retinal and Ocular Therapeutics, F.M. Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
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44
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Abstract
The extraction of statistically meaningful quantitative information from microscopy images is increasingly important for modern biological research. Obtaining accurate, quantitative information from biological specimens, however, is a complex process that requires optimization of several parameters. One must consider the number of probes, fluorescent channels required, type of plate to be used, number of fields to be acquired and optimal resolution for image acquisition. The extraction of information from images is dependent on and can be aided greatly by careful consideration of the factors involved in the image acquisition process. I summarize here the general principles behind the imaging and software technology that is used to quantify images and highlight particular issues of concern for critically applying image quantitation techniques for research.
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Affiliation(s)
- P J Gokhale
- a Department of Biomedical Science , University of Sheffield , Western Bank, Sheffield , United Kingdom
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45
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O'Brien CM, Chy HS, Zhou Q, Blumenfeld S, Lambshead JW, Liu X, Kie J, Capaldo BD, Chung TL, Adams TE, Phan T, Bentley JD, McKinstry WJ, Oliva K, McMurrick PJ, Wang YC, Rossello FJ, Lindeman GJ, Chen D, Jarde T, Clark AT, Abud HE, Visvader JE, Nefzger CM, Polo JM, Loring JF, Laslett AL. New Monoclonal Antibodies to Defined Cell Surface Proteins on Human Pluripotent Stem Cells. Stem Cells 2017; 35:626-640. [PMID: 28009074 PMCID: PMC5412944 DOI: 10.1002/stem.2558] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 10/31/2016] [Accepted: 11/18/2016] [Indexed: 01/28/2023]
Abstract
The study and application of human pluripotent stem cells (hPSCs) will be enhanced by the availability of well‐characterized monoclonal antibodies (mAbs) detecting cell‐surface epitopes. Here, we report generation of seven new mAbs that detect cell surface proteins present on live and fixed human ES cells (hESCs) and human iPS cells (hiPSCs), confirming our previous prediction that these proteins were present on the cell surface of hPSCs. The mAbs all show a high correlation with POU5F1 (OCT4) expression and other hPSC surface markers (TRA‐160 and SSEA‐4) in hPSC cultures and detect rare OCT4 positive cells in differentiated cell cultures. These mAbs are immunoreactive to cell surface protein epitopes on both primed and naive state hPSCs, providing useful research tools to investigate the cellular mechanisms underlying human pluripotency and states of cellular reprogramming. In addition, we report that subsets of the seven new mAbs are also immunoreactive to human bone marrow‐derived mesenchymal stem cells (MSCs), normal human breast subsets and both normal and tumorigenic colorectal cell populations. The mAbs reported here should accelerate the investigation of the nature of pluripotency, and enable development of robust cell separation and tracing technologies to enrich or deplete for hPSCs and other human stem and somatic cell types. Stem Cells2017;35:626–640
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Affiliation(s)
- Carmel M O'Brien
- Clayton and Parkville, CSIRO Manufacturing, Victoria, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Hun S Chy
- Clayton and Parkville, CSIRO Manufacturing, Victoria, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Qi Zhou
- Clayton and Parkville, CSIRO Manufacturing, Victoria, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | | | - Jack W Lambshead
- Clayton and Parkville, CSIRO Manufacturing, Victoria, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Xiaodong Liu
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia.,Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
| | - Joshua Kie
- Clayton and Parkville, CSIRO Manufacturing, Victoria, Australia.,Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
| | - Bianca D Capaldo
- The Walter and Eliza Hall Institute (WEHI), Parkville, Victoria, Australia.,Department of Medical Biology
| | - Tung-Liang Chung
- Clayton and Parkville, CSIRO Manufacturing, Victoria, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Timothy E Adams
- Clayton and Parkville, CSIRO Manufacturing, Victoria, Australia
| | - Tram Phan
- Clayton and Parkville, CSIRO Manufacturing, Victoria, Australia
| | - John D Bentley
- Clayton and Parkville, CSIRO Manufacturing, Victoria, Australia
| | | | - Karen Oliva
- Department of Surgery, Cabrini Monash University, Malvern, Victoria, Australia
| | - Paul J McMurrick
- Department of Surgery, Cabrini Monash University, Malvern, Victoria, Australia
| | - Yu-Chieh Wang
- Department of Chemical Physiology.,Center for Regenerative Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - Fernando J Rossello
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia.,Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
| | - Geoffrey J Lindeman
- The Walter and Eliza Hall Institute (WEHI), Parkville, Victoria, Australia.,Department of Medicine, The University of Melbourne, Parkville, Victoria, Australia.,Department of Medical Oncology, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Di Chen
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, USA
| | - Thierry Jarde
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia.,Cancer Program, Monash Biomedicine Discovery Institute.,Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia
| | - Amander T Clark
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, USA
| | - Helen E Abud
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia.,Cancer Program, Monash Biomedicine Discovery Institute
| | - Jane E Visvader
- The Walter and Eliza Hall Institute (WEHI), Parkville, Victoria, Australia.,Department of Medical Biology
| | - Christian M Nefzger
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia.,Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
| | - Jose M Polo
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia.,Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
| | - Jeanne F Loring
- Department of Chemical Physiology.,Center for Regenerative Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - Andrew L Laslett
- Clayton and Parkville, CSIRO Manufacturing, Victoria, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
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Balachandar V, Dhivya V, Gomathi M, Mohanadevi S, Venkatesh B, Geetha B. A review of Rett syndrome (RTT) with induced pluripotent stem cells. Stem Cell Investig 2016; 3:52. [PMID: 27777941 DOI: 10.21037/sci.2016.09.05] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 09/08/2016] [Indexed: 11/06/2022]
Abstract
Human induced pluripotent stem cells (hiPSCs) are pluripotent stem cells generated from somatic cells by the introduction of a combination of pluripotency-associated genes such as OCT4, SOX2, along with either KLF4 and c-MYC or NANOG and LIN28 via retroviral or lentiviral vectors. Most importantly, hiPSCs are similar to human embryonic stem cells (hESCs) functionally as they are pluripotent and can potentially differentiate into any desired cell type when provided with the appropriate cues, but do not have the ethical issues surrounding hESCs. For these reasons, hiPSCs have huge potential in translational medicine such as disease modeling, drug screening, and cellular therapy. Indeed, patient-specific hiPSCs have been generated for a multitude of diseases, including many with a neurological basis, in which disease phenotypes have been recapitulated in vitro and proof-of-principle drug screening has been performed. As the techniques for generating hiPSCs are refined and these cells become a more widely used tool for understanding brain development, the insights they produce must be understood in the context of the greater complexity of the human genome and the human brain. Disease models using iPS from Rett syndrome (RTT) patient's fibroblasts have opened up a new avenue of drug discovery for therapeutic treatment of RTT. The analysis of X chromosome inactivation (XCI) upon differentiation of RTT-hiPSCs into neurons will be critical to conclusively demonstrate the isolation of pre-XCI RTT-hiPSCs in comparison to post-XCI RTT-hiPSCs. The current review projects on iPSC studies in RTT as well as XCI in hiPSC were it suggests for screening new potential therapeutic targets for RTT in future for the benefit of RTT patients. In conclusion, patient-specific drug screening might be feasible and would be particularly helpful in disorders where patients frequently have to try multiple drugs before finding a regimen that works.
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Affiliation(s)
- Vellingiri Balachandar
- Human Molecular Genetics and Stem Cell Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore-641 046, Tamil Nadu, India
| | - Venkatesan Dhivya
- Human Molecular Genetics and Stem Cell Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore-641 046, Tamil Nadu, India
| | - Mohan Gomathi
- Human Molecular Genetics and Stem Cell Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore-641 046, Tamil Nadu, India
| | - Subramaniam Mohanadevi
- Human Molecular Genetics and Stem Cell Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore-641 046, Tamil Nadu, India
| | - Balasubramanian Venkatesh
- Human Molecular Genetics and Stem Cell Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore-641 046, Tamil Nadu, India
| | - Bharathi Geetha
- Human Molecular Genetics and Stem Cell Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore-641 046, Tamil Nadu, India
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47
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Parametric analysis of colony morphology of non-labelled live human pluripotent stem cells for cell quality control. Sci Rep 2016; 6:34009. [PMID: 27667091 PMCID: PMC5036041 DOI: 10.1038/srep34009] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/06/2016] [Indexed: 11/17/2022] Open
Abstract
Given the difficulties inherent in maintaining human pluripotent stem cells (hPSCs) in a healthy state, hPSCs should be routinely characterized using several established standard criteria during expansion for research or therapeutic purposes. hPSC colony morphology is typically considered an important criterion, but it is not evaluated quantitatively. Thus, we designed an unbiased method to evaluate hPSC colony morphology. This method involves a combination of automated non-labelled live-cell imaging and the implementation of morphological colony analysis algorithms with multiple parameters. To validate the utility of the quantitative evaluation method, a parent cell line exhibiting typical embryonic stem cell (ESC)-like morphology and an aberrant hPSC subclone demonstrating unusual colony morphology were used as models. According to statistical colony classification based on morphological parameters, colonies containing readily discernible areas of differentiation constituted a major classification cluster and were distinguishable from typical ESC-like colonies; similar results were obtained via classification based on global gene expression profiles. Thus, the morphological features of hPSC colonies are closely associated with cellular characteristics. Our quantitative evaluation method provides a biological definition of ‘hPSC colony morphology’, permits the non-invasive monitoring of hPSC conditions and is particularly useful for detecting variations in hPSC heterogeneity.
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48
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Garcia-Martinez J, Bakker B, Schukken KM, Simon JE, Foijer F. Aneuploidy in stem cells. World J Stem Cells 2016; 8:216-222. [PMID: 27354891 PMCID: PMC4919689 DOI: 10.4252/wjsc.v8.i6.216] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 02/16/2016] [Accepted: 03/18/2016] [Indexed: 02/06/2023] Open
Abstract
Stem cells hold enormous promise for regenerative medicine as well as for engineering of model systems to study diseases and develop new drugs. The discovery of protocols that allow for generating induced pluripotent stem cells (IPSCs) from somatic cells has brought this promise steps closer to reality. However, as somatic cells might have accumulated various chromosomal abnormalities, including aneuploidies throughout their lives, the resulting IPSCs might no longer carry the perfect blueprint for the tissue to be generated, or worse, become at risk of adopting a malignant fate. In this review, we discuss the contribution of aneuploidy to healthy tissues and how aneuploidy can lead to disease. Furthermore, we review the differences between how somatic cells and stem cells respond to aneuploidy.
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49
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RNA Polymerase III Advances: Structural and tRNA Functional Views. Trends Biochem Sci 2016; 41:546-559. [PMID: 27068803 DOI: 10.1016/j.tibs.2016.03.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 03/03/2016] [Accepted: 03/09/2016] [Indexed: 12/25/2022]
Abstract
RNA synthesis in eukaryotes is divided among three RNA polymerases (RNAPs). RNAP III transcribes hundreds of tRNA genes and fewer additional short RNA genes. We survey recent work on transcription by RNAP III including an atomic structure, mechanisms of action, interactions with chromatin and retroposons, and a conserved link between its activity and a tRNA modification that enhances mRNA decoding. Other new work suggests important mechanistic connections to oxidative stress, autoimmunity and cancer, embryonic stem cell pluripotency, and tissue-specific developmental effects. We consider that, for some of its complex functions, variation in RNAP III activity levels lead to nonuniform changes in tRNAs that can shift the translation profiles of key codon-biased mRNAs with resultant phenotypes or disease states.
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50
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Burns AJ, Goldstein AM, Newgreen DF, Stamp L, Schäfer KH, Metzger M, Hotta R, Young HM, Andrews PW, Thapar N, Belkind-Gerson J, Bondurand N, Bornstein JC, Chan WY, Cheah K, Gershon MD, Heuckeroth RO, Hofstra RMW, Just L, Kapur RP, King SK, McCann CJ, Nagy N, Ngan E, Obermayr F, Pachnis V, Pasricha PJ, Sham MH, Tam P, Vanden Berghe P. White paper on guidelines concerning enteric nervous system stem cell therapy for enteric neuropathies. Dev Biol 2016; 417:229-51. [PMID: 27059883 DOI: 10.1016/j.ydbio.2016.04.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 03/29/2016] [Accepted: 04/02/2016] [Indexed: 12/22/2022]
Abstract
Over the last 20 years, there has been increasing focus on the development of novel stem cell based therapies for the treatment of disorders and diseases affecting the enteric nervous system (ENS) of the gastrointestinal tract (so-called enteric neuropathies). Here, the idea is that ENS progenitor/stem cells could be transplanted into the gut wall to replace the damaged or absent neurons and glia of the ENS. This White Paper sets out experts' views on the commonly used methods and approaches to identify, isolate, purify, expand and optimize ENS stem cells, transplant them into the bowel, and assess transplant success, including restoration of gut function. We also highlight obstacles that must be overcome in order to progress from successful preclinical studies in animal models to ENS stem cell therapies in the clinic.
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Affiliation(s)
- Alan J Burns
- Stem Cells and Regenerative Medicine, UCL Great Ormond Street Institute of Child Health, London, UK; Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands.
| | - Allan M Goldstein
- Department of Pediatric Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Donald F Newgreen
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville 3052, Victoria, Australia
| | - Lincon Stamp
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Karl-Herbert Schäfer
- University of Applied Sciences, Kaiserlautern, Germany; Clinic of Pediatric Surgery, University Hospital Mannheim, University Heidelberg, Germany
| | - Marco Metzger
- Fraunhofer-Institute Interfacial Engineering and Biotechnology IGB Translational Centre - Würzburg branch and University Hospital Würzburg - Tissue Engineering and Regenerative Medicine (TERM), Würzburg, Germany
| | - Ryo Hotta
- Department of Pediatric Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Heather M Young
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Peter W Andrews
- Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Sheffield, UK
| | - Nikhil Thapar
- Stem Cells and Regenerative Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Jaime Belkind-Gerson
- Division of Gastroenterology, Hepatology and Nutrition, Massachusetts General Hospital for Children, Harvard Medical School, Boston, USA
| | - Nadege Bondurand
- INSERM U955, 51 Avenue du Maréchal de Lattre de Tassigny, F-94000 Créteil, France; Université Paris-Est, UPEC, F-94000 Créteil, France
| | - Joel C Bornstein
- Department of Physiology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Wood Yee Chan
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong
| | - Kathryn Cheah
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong
| | - Michael D Gershon
- Department of Pathology and Cell Biology, Columbia University, New York 10032, USA
| | - Robert O Heuckeroth
- Department of Pediatrics, The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Perelman School of Medicine at the University of Pennsylvania, Abramson Research Center, Philadelphia, PA 19104, USA
| | - Robert M W Hofstra
- Stem Cells and Regenerative Medicine, UCL Great Ormond Street Institute of Child Health, London, UK; Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lothar Just
- Institute of Clinical Anatomy and Cell Analysis, University of Tübingen, Germany
| | - Raj P Kapur
- Department of Pathology, University of Washington and Seattle Children's Hospital, Seattle, WA, USA
| | - Sebastian K King
- Department of Paediatric and Neonatal Surgery, The Royal Children's Hospital, Melbourne, Australia
| | - Conor J McCann
- Stem Cells and Regenerative Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Nandor Nagy
- Department of Anatomy, Histology and Embryology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Elly Ngan
- Department of Surgery, The University of Hong Kong, Hong Kong
| | - Florian Obermayr
- Department of Pediatric Surgery and Pediatric Urology, University Children's Hospital Tübingen, D-72076 Tübingen, Germany
| | | | | | - Mai Har Sham
- Department of Biochemistry, The University of Hong Kong, Hong Kong
| | - Paul Tam
- Department of Surgery, The University of Hong Kong, Hong Kong
| | - Pieter Vanden Berghe
- Laboratory for Enteric NeuroScience (LENS), TARGID, University of Leuven, Belgium
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