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Liu Y, Han T, Miao R, Zhou J, Guo J, Xu Z, Xing Y, Bai Y, Wu J, Hu D. RACGAP1 promotes the progression and poor prognosis of lung adenocarcinoma through its effects on the cell cycle and tumor stemness. BMC Cancer 2024; 24:7. [PMID: 38167018 PMCID: PMC10763365 DOI: 10.1186/s12885-023-11761-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
OBJECTION Investigating the key genes and mechanisms that influence stemness in lung adenocarcinoma. METHODS First, consistent clustering analysis was performed on lung adenocarcinoma patients using stemness scoring to classify them. Subsequently, WGCNA was utilized to identify key modules and hub genes. Then, machine learning methods were employed to screen and identify the key genes within these modules. Lastly, functional analysis of the key genes was conducted through cell scratch assays, colony formation assays, transwell migration assays, flow cytometry cell cycle analysis, and xenograft tumor models. RESULTS First, two groups of patients with different stemness scores were obtained, where the high stemness score group exhibited poor prognosis and immunotherapy efficacy. Next, LASSO regression analysis and random forest regression were employed to identify genes (PBK, RACGAP1) associated with high stemness scores. RACGAP1 was significantly upregulated in the high stemness score group of lung adenocarcinoma and closely correlated with clinical pathological features, poor overall survival (OS), recurrence-free survival (RFS), and unfavorable prognosis in lung adenocarcinoma patients. Knockdown of RACGAP1 suppressed the migration, proliferation, and tumor growth of cancer cells. CONCLUSION RACGAP1 not only indicates poor prognosis and limited immunotherapy benefits but also serves as a potential targeted biomarker influencing tumor stemness.
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Affiliation(s)
- Yafeng Liu
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, P.R. China
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, P.R. China
| | - Tao Han
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, P.R. China
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, P.R. China
| | - Rui Miao
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, P.R. China
| | - Jiawei Zhou
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, P.R. China
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, P.R. China
| | - Jianqiang Guo
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, P.R. China
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, P.R. China
| | - Zhi Xu
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, P.R. China
| | - Yingru Xing
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, P.R. China
- Department of Clinical Laboratory, Anhui Zhongke Gengjiu Hospital, Hefei, P.R. China
| | - Ying Bai
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, P.R. China.
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, P.R. China.
| | - Jing Wu
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, P.R. China.
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, P.R. China.
| | - Dong Hu
- School of Medicine, Anhui University of Science and Technology, Chongren Building, No 168, Taifeng St, Huainan, 232001, P.R. China.
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Huainan, P.R. China.
- Key Laboratory of Industrial Dust Prevention and Control & Occupational Safety and Health of the Ministry of Education, Anhui University of Science and Technology, Huainan, P.R. China.
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2
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Milagre I, Pereira C, Oliveira RA. Compromised Mitotic Fidelity in Human Pluripotent Stem Cells. Int J Mol Sci 2023; 24:11933. [PMID: 37569309 PMCID: PMC10418648 DOI: 10.3390/ijms241511933] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
Human pluripotent stem cells (PSCs), which include both embryonic and induced pluripotent stem cells, are widely used in fundamental and applied biomedical research. They have been instrumental for better understanding development and cell differentiation processes, disease origin and progression and can aid in the discovery of new drugs. PSCs also hold great potential in regenerative medicine to treat or diminish the effects of certain debilitating diseases, such as degenerative disorders. However, some concerns have recently been raised over their safety for use in regenerative medicine. One of the major concerns is the fact that PSCs are prone to errors in passing the correct number of chromosomes to daughter cells, resulting in aneuploid cells. Aneuploidy, characterised by an imbalance in chromosome number, elicits the upregulation of different stress pathways that are deleterious to cell homeostasis, impair proper embryo development and potentiate cancer development. In this review, we will summarize known molecular mechanisms recently revealed to impair mitotic fidelity in human PSCs and the consequences of the decreased mitotic fidelity of these cells. We will finish with speculative views on how the physiological characteristics of PSCs can affect the mitotic machinery and how their suboptimal mitotic fidelity may be circumvented.
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Affiliation(s)
- Inês Milagre
- Católica Biomedical Research Centre, Católica Medical School, Universidade Católica Portuguesa, 1649-023 Lisbon, Portugal
| | | | - Raquel A. Oliveira
- Católica Biomedical Research Centre, Católica Medical School, Universidade Católica Portuguesa, 1649-023 Lisbon, Portugal
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
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3
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Fedorova V, Amruz Cerna K, Oppelt J, Pospisilova V, Barta T, Mraz M, Bohaciakova D. MicroRNA Profiling of Self-Renewing Human Neural Stem Cells Reveals Novel Sets of Differentially Expressed microRNAs During Neural Differentiation In Vitro. Stem Cell Rev Rep 2023:10.1007/s12015-023-10524-2. [PMID: 36918496 PMCID: PMC10366325 DOI: 10.1007/s12015-023-10524-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2023] [Indexed: 03/16/2023]
Abstract
The involvement of microRNAs (miRNAs) in orchestrating self-renewal and differentiation of stem cells has been revealed in a number of recent studies. And while in human pluripotent stem cells, miRNAs have been directly linked to the core pluripotency network, including the cell cycle regulation and the maintenance of the self-renewing capacity, their role in the onset of differentiation in other contexts, such as determination of neural cell fate, remains poorly described. To bridge this gap, we used three model cell types to study miRNA expression patterns: human embryonic stem cells (hESCs), hESCs-derived self-renewing neural stem cells (NSCs), and differentiating NSCs. The comprehensive miRNA profiling presented here reveals novel sets of miRNAs differentially expressed during human neural cell fate determination in vitro. Furthermore, we report a miRNA expression profile of self-renewing human NSCs, which has been lacking to this date. Our data also indicates that miRNA clusters enriched in NSCs share the target-determining seed sequence with cell cycle regulatory miRNAs expressed in pluripotent hESCs. Lastly, our mechanistic experiments confirmed that cluster miR-17-92, one of the NSCs-enriched clusters, is directly transcriptionally regulated by transcription factor c-MYC.
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Affiliation(s)
- Veronika Fedorova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Katerina Amruz Cerna
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jan Oppelt
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Veronika Pospisilova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Tomas Barta
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Marek Mraz
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Dasa Bohaciakova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic. .,International Clinical Research Center (ICRC), St. Anne's University Hospital, Brno, Czech Republic.
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4
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Nakanoh S, Kadiwala J, Pinte L, Morell CM, Lenaerts AS, Vallier L. Simultaneous depletion of RB, RBL1 and RBL2 affects endoderm differentiation of human embryonic stem cells. PLoS One 2022; 17:e0269122. [PMID: 36413521 PMCID: PMC9681086 DOI: 10.1371/journal.pone.0269122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 05/16/2022] [Indexed: 11/23/2022] Open
Abstract
RB is a well-known cell cycle regulator controlling the G1 checkpoint. Previous reports have suggested that it can influence cell fate decisions not only by regulating cell proliferation and survival but also by interacting with transcription factors and epigenetic modifiers. However, the functional redundancy of RB family proteins (RB, RBL1 and RBL2) renders it difficult to investigate their roles during early development, especially in human. Here, we address this problem by generating human embryonic stem cells lacking RB family proteins. To achieve this goal, we first introduced frameshift mutations in RBL1 and RBL2 genes using the CRISPR/Cas9 technology, and then integrated the shRNA-expression cassette to knockdown RB upon tetracycline treatment. The resulting RBL1/2_dKO+RB_iKD cells remain pluripotent and efficiently differentiate into the primary germ layers in vitro even in the absence of the RB family proteins. In contrast, we observed that subsequent differentiation into foregut endoderm was impaired without the expression of RB, RBL1 and RBL2. Thus, it is suggested that RB proteins are dispensable for the maintenance and acquisition of cell identities during early development, but they are essential to generate advanced derivatives after the formation of primary germ layers. These results also indicate that our RBL1/2_dKO+RB_iKD cell lines are useful to depict the detailed molecular roles of RB family proteins in the maintenance and generation of various cell types accessible from human pluripotent stem cells.
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Affiliation(s)
- Shota Nakanoh
- Division of Embryology, National Institute for Basic Biology, Okazaki, Aichi, Japan
- Wellcome Trust–MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Surgery, University of Cambridge, Cambridge, United Kingdom
| | - Juned Kadiwala
- National Institute for Health and Care Research Cambridge Biomedical Research Centre Human Induced Pluripotent Stem Cells Core Facility, University of Cambridge, Cambridge, United Kingdom
| | - Laetitia Pinte
- Wellcome Trust–MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Surgery, University of Cambridge, Cambridge, United Kingdom
| | - Carola Maria Morell
- Wellcome Trust–MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Surgery, University of Cambridge, Cambridge, United Kingdom
| | - An-Sofie Lenaerts
- National Institute for Health and Care Research Cambridge Biomedical Research Centre Human Induced Pluripotent Stem Cells Core Facility, University of Cambridge, Cambridge, United Kingdom
| | - Ludovic Vallier
- Wellcome Trust–MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Surgery, University of Cambridge, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
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5
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Perera M, Nissen SB, Proks M, Pozzi S, Monteiro RS, Trusina A, Brickman JM. Transcriptional heterogeneity and cell cycle regulation as central determinants of primitive endoderm priming. eLife 2022; 11:78967. [PMID: 35969041 PMCID: PMC9417417 DOI: 10.7554/elife.78967] [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: 03/25/2022] [Accepted: 08/12/2022] [Indexed: 11/16/2022] Open
Abstract
During embryonic development cells acquire identity as they proliferate, implying that an intrinsic facet of cell fate choice requires coupling lineage decisions to cell division. How is the cell cycle regulated to promote or suppress heterogeneity and differentiation? We explore this question combining time lapse imaging with single-cell RNA-seq in the contexts of self-renewal, priming, and differentiation of mouse embryonic stem cells (ESCs) towards the Primitive Endoderm (PrE) lineage. Since ESCs are derived from the inner cell mass (ICM) of the mammalian blastocyst, ESCs in standard culture conditions are transcriptionally heterogeneous containing dynamically interconverting subfractions primed for either of the two ICM lineages, Epiblast and PrE. Here, we find that differential regulation of cell cycle can tip the balance between these primed populations, such that naïve ESC culture promotes Epiblast-like expansion and PrE differentiation stimulates the selective survival and proliferation of PrE-primed cells. In endoderm differentiation, this change is accompanied by a counter-intuitive increase in G1 length, also observed in vivo. While fibroblast growth factor/extracellular signal-regulated kinase (FGF/ERK) signalling is a key regulator of ESC differentiation and PrE specification, we find it is not just responsible for ESCs heterogeneity, but also the inheritance of similar cell cycles between sisters and cousins. Taken together, our results indicate a tight relationship between transcriptional heterogeneity and cell cycle regulation in lineage specification, with primed cell populations providing a pool of flexible cell types that can be expanded in a lineage-specific fashion while allowing plasticity during early determination.
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Affiliation(s)
- Marta Perera
- The Novo Nordisk Foundation Center for Stem Cell Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | - Martin Proks
- The Novo Nordisk Foundation Center for Stem Cell Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Sara Pozzi
- The Novo Nordisk Foundation Center for Stem Cell Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Rita Soares Monteiro
- The Novo Nordisk Foundation Center for Stem Cell Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ala Trusina
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Joshua M Brickman
- The Novo Nordisk Foundation Center for Stem Cell Medicine, University of Copenhagen, Copenhagen, Denmark
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6
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Sánchez-Botet A, Quandt E, Masip N, Escribá R, Novellasdemunt L, Gasa L, Li VSW, Raya Á, Clotet J, Ribeiro MPC. Atypical cyclin P regulates cancer cell stemness through activation of the WNT pathway. Cell Oncol (Dordr) 2021; 44:1273-1286. [PMID: 34604945 PMCID: PMC8648692 DOI: 10.1007/s13402-021-00636-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2021] [Indexed: 12/24/2022] Open
Abstract
PURPOSE Cancer stem cells represent a cancer cell subpopulation that has been found to be associated with metastasis and chemoresistance. Therefore, it is vital to identify mechanisms regulating cancer stemness. Previously, we have shown that the atypical cyclin P (CCNP), also known as CNTD2, is upregulated in lung and colorectal cancers and is associated with a worse clinical prognosis. Given that other cyclins have been implicated in pluripotency regulation, we hypothesized that CCNP may also play a role in cancer stemness. METHODS Cell line-derived spheroids, ex vivo intestinal organoid cultures and induced-pluripotent stem cells (iPSCs) were used to investigate the role of CCNP in stemness. The effects of CCNP on cancer cell stemness and the expression of pluripotency markers and ATP-binding cassette (ABC) transporters were evaluated using Western blotting and RT-qPCR assays. Cell viability was assessed using a MTT assay. The effects of CCNP on WNT targets were monitored by RNA-seq analysis. Data from publicly available web-based resources were also analyzed. RESULTS We found that CCNP increases spheroid formation in breast, lung and colorectal cancers, and upregulates the expression of stemness (CD44, CD133) and pluripotency (SOX2, OCT4, NANOG) markers. In addition, we found that CCNP promotes resistance to anticancer drugs and induces the expression of multidrug resistance ABC transporters. Our RNA-seq data indicate that CCNP activates the WNT pathway, and that inhibition of this pathway abrogates the increase in spheroid formation promoted by CCNP. Finally, we found that CCNP knockout decreases OCT4 expression in iPSCs, further supporting the notion that CCNP is involved in stemness regulation. CONCLUSION Our results reveal CCNP as a novel player in stemness and as a potential therapeutic target in cancer.
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Affiliation(s)
- Abril Sánchez-Botet
- Department of Basic Sciences, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Josep Trueta, s/n, 08195, Sant Cugat del Vallès, Barcelona, Spain
| | - Eva Quandt
- Department of Basic Sciences, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Josep Trueta, s/n, 08195, Sant Cugat del Vallès, Barcelona, Spain
| | - Núria Masip
- Department of Basic Sciences, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Josep Trueta, s/n, 08195, Sant Cugat del Vallès, Barcelona, Spain
| | - Rubén Escribá
- Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL) and Program for Clinical Translation of Regenerative Medicine in Catalonia (P-CMRC), L'Hospitalet del Llobregat, Barcelona, Spain
- Centre for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - Laura Novellasdemunt
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute, London, UK
| | - Laura Gasa
- Department of Basic Sciences, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Josep Trueta, s/n, 08195, Sant Cugat del Vallès, Barcelona, Spain
| | - Vivian S W Li
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute, London, UK
| | - Ángel Raya
- Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL) and Program for Clinical Translation of Regenerative Medicine in Catalonia (P-CMRC), L'Hospitalet del Llobregat, Barcelona, Spain
- Centre for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Josep Clotet
- Department of Basic Sciences, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Josep Trueta, s/n, 08195, Sant Cugat del Vallès, Barcelona, Spain.
| | - Mariana P C Ribeiro
- Department of Basic Sciences, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Josep Trueta, s/n, 08195, Sant Cugat del Vallès, Barcelona, Spain.
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7
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Wang J, Mongan M, Zhang X, Xia Y. Isolation and long-term expansion of murine epidermal stem-like cells. PLoS One 2021; 16:e0254731. [PMID: 34270586 PMCID: PMC8284819 DOI: 10.1371/journal.pone.0254731] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/01/2021] [Indexed: 11/19/2022] Open
Abstract
Epidermis is the most outer layer of the skin and a physical barrier protecting the internal tissues from mechanical and environmental insults. The basal keratinocytes, which, through proliferation and differentiation, supply diverse cell types for epidermal homeostasis and injury repair. Sustainable culture of murine keratinocyte, however, is a major obstacle. Here we developed murine keratinocyte lines using low-Ca2+ (0.06 mM) keratinocyte serum-free medium (KSFM-Ca2+) without feeder cells. Cells derived in this condition could be subcultured for >70 passages. They displayed basal epithelial cell morphology and expressed keratin (Krt) 14, but lacked the epithelial-characteristic intercellular junctions. Moreover, these cells could be adapted to grow in the Defined-KSFM (DKSFM) media containing 0.15 mM Ca2+, and the adapted cells established tight- and adherens-junctions and exhibited increased Krt1/10 expression while retained subculture capacity. Global gene expression studies showed cells derived in KSFM-Ca2+ media had enriched stem/proliferation markers and cells adapted in DKSFM media had epithelial progenitor signatures. Correspondingly, KSFM-Ca2+-derived cells exhibited a remarkable capacity of clonal expansion, whereas DKSFM-adapted cells could differentiate to suprabasal epithelial cell types in 3-dimentional (3D) organoids. The generation of stem-like murine keratinocyte lines and the conversion of these cells to epithelial progenitors capable of terminal differentiation provide the critically needed resources for skin research.
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Affiliation(s)
- Jingjing Wang
- Department of Environmental and Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Maureen Mongan
- Department of Environmental and Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Xiang Zhang
- Department of Environmental and Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Ying Xia
- Department of Environmental and Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, Ohio, United States of America
- * E-mail:
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8
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Li HD, Xu Y, Zhu X, Liu Q, Omenn GS, Wang J. ClusterMine: A knowledge-integrated clustering approach based on expression profiles of gene sets. J Bioinform Comput Biol 2021; 18:2040009. [PMID: 32698720 DOI: 10.1142/s0219720020400090] [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] [Indexed: 01/01/2023]
Abstract
Clustering analysis of gene expression data is essential for understanding complex biological data, and is widely used in important biological applications such as the identification of cell subpopulations and disease subtypes. In commonly used methods such as hierarchical clustering (HC) and consensus clustering (CC), holistic expression profiles of all genes are often used to assess the similarity between samples for clustering. While these methods have been proven successful in identifying sample clusters in many areas, they do not provide information about which gene sets (functions) contribute most to the clustering, thus limiting the interpretability of the resulting cluster. We hypothesize that integrating prior knowledge of annotated gene sets would not only achieve satisfactory clustering performance but also, more importantly, enable potential biological interpretation of clusters. Here we report ClusterMine, an approach that identifies clusters by assessing functional similarity between samples through integrating known annotated gene sets in functional annotation databases such as Gene Ontology. In addition to the cluster membership of each sample as provided by conventional approaches, it also outputs gene sets that most likely contribute to the clustering, thus facilitating biological interpretation. We compare ClusterMine with conventional approaches on nine real-world experimental datasets that represent different application scenarios in biology. We find that ClusterMine achieves better performances and that the gene sets prioritized by our method are biologically meaningful. ClusterMine is implemented as an R package and is freely available at: www.genemine.org/clustermine.php.
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Affiliation(s)
- Hong-Dong Li
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 400083, P. R. China
| | - Yunpei Xu
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 400083, P. R. China
| | - Xiaoshu Zhu
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 400083, P. R. China.,School of Computer Science and Engineering, Yulin Normal University, Yulin, Guangxi, P. R. China
| | - Quan Liu
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 400083, P. R. China
| | - Gilbert S Omenn
- Departments of Computational Medicine and Bioinformatics, Internal Medicine, Human Genetics and School of Public Health, University of Michigan, Ann Arbor, MI 48109-2218, USA
| | - Jianxin Wang
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 400083, P. R. China
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Kim K, Park S, Kim H, Min S, Ku S, Seo J, Roh S. Enterococcus faecium L-15 Extract Enhances the Self-Renewal and Proliferation of Mouse Skin-Derived Precursor Cells. Probiotics Antimicrob Proteins 2021; 12:1492-1501. [PMID: 32162154 DOI: 10.1007/s12602-020-09635-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Lactic acid bacteria (LAB) in the gastrointestinal tract have beneficial health effects. LAB activate the proliferation of intestinal stem cells and speed the recovery of damaged intestinal cells, but little is known about effect of LAB on other adult stem cells. In this study, a cell-free extract of Enterococcus faecium L-15 (L15) was exposed to mouse skin-derived precursor cells (SKPs), and the changes in characteristics associated with proliferation and self-renewal capacity were investigated. L15 increased the size of the spheres and the proliferation rate of SKPs. Cell cycle analysis revealed that cells in the S-phase increased after treatment with L15. In the L15-treated group, the total number of spheres significantly increased. The expression level of pluripotency marker genes also increased, while the mesenchymal lineage-related differentiation marker genes significantly decreased in the L15-treated group. The PI3K/Akt signaling pathway was activated by L15 in SKPs. These results indicate that L15 enhances proliferation and self-renewal of SKPs and may be used as a supplement for stem cell maintenance or application of stem cell therapy. This is the first report to investigate the functional effects of E. faecium on the proliferation and self-renewal capacity of SKPs.
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Affiliation(s)
- Kichul Kim
- Cellular Reprogramming and Embryo Biotechnology Laboratory, Dental Research Institute, BK21, Seoul National University School of Dentistry, Seoul, 08826, South Korea
| | - Sangkyu Park
- Cellular Reprogramming and Embryo Biotechnology Laboratory, Dental Research Institute, BK21, Seoul National University School of Dentistry, Seoul, 08826, South Korea.,Biomedical Research Institute, Neoregen Biotech Co., Ltd., Gyeonggi-do, 16614, South Korea
| | - Hyewon Kim
- Cellular Reprogramming and Embryo Biotechnology Laboratory, Dental Research Institute, BK21, Seoul National University School of Dentistry, Seoul, 08826, South Korea
| | - Sol Min
- Cellular Reprogramming and Embryo Biotechnology Laboratory, Dental Research Institute, BK21, Seoul National University School of Dentistry, Seoul, 08826, South Korea
| | - Seockmo Ku
- Fermentation Science Program, School of Agriculture, College of Basic and Applied Sciences, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Jeongmin Seo
- Cellular Reprogramming and Embryo Biotechnology Laboratory, Dental Research Institute, BK21, Seoul National University School of Dentistry, Seoul, 08826, South Korea. .,Biomedical Research Institute, Neoregen Biotech Co., Ltd., Gyeonggi-do, 16614, South Korea.
| | - Sangho Roh
- Cellular Reprogramming and Embryo Biotechnology Laboratory, Dental Research Institute, BK21, Seoul National University School of Dentistry, Seoul, 08826, South Korea.
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10
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Halliwell JA, Gravells P, Bryant HE. DNA Fiber Assay for the Analysis of DNA Replication Progression in Human Pluripotent Stem Cells. ACTA ACUST UNITED AC 2021; 54:e115. [PMID: 32584505 DOI: 10.1002/cpsc.115] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Human pluripotent stem cells (PSC) acquire recurrent chromosomal instabilities during prolonged in vitro culture that threaten to preclude their use in cell-based regenerative medicine. The rapid proliferation of pluripotent cells leads to constitutive replication stress, hindering the progression of DNA replication forks and in some cases leading to replication-fork collapse. Failure to overcome replication stress can result in incomplete genome duplication, which, if left to persist into the subsequent mitosis, can result in structural and numerical chromosomal instability. We have recently applied the DNA fiber assay to the study of replication stress in human PSC and found that, in comparison to somatic cells states, these cells display features of DNA replication stress that include slower replication fork speeds, evidence of stalled forks, and replication initiation from dormant replication origins. These findings have expanded on previous work demonstrating that extensive DNA damage in human PSC is replication associated. In this capacity, the DNA fiber assay has enabled the development of an advanced nucleoside-enriched culture medium that increases replication fork progression and decreases DNA damage and mitotic errors in human PSC cultures. The DNA fiber assay allows for the study of replication fork dynamics at single-molecule resolution. The assay relies on cells incorporating nucleotide analogs into nascent DNA during replication, which are then measured to monitor several replication parameters. Here we provide an optimized protocol for the fiber assay intended for use with human PSC, and describe the methods employed to analyze replication fork parameters. © 2020 Wiley Periodicals LLC. Basic Protocol 1: DNA fiber labeling Basic Protocol 2: DNA fiber spreading Basic Protocol 3: Immunostaining Support Protocol 1: Microscopy/data acquisition Support Protocol 2: Data analysis.
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Affiliation(s)
- Jason A Halliwell
- The Centre for Stem Cell Biology, University of Sheffield, Department of Biomedical Science, Sheffield, United Kingdom
| | - Polly Gravells
- Academic Unit of Molecular Oncology, Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
| | - Helen E Bryant
- Academic Unit of Molecular Oncology, Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
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11
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Ter Huurne M, Stunnenberg HG. G1-phase progression in pluripotent stem cells. Cell Mol Life Sci 2021; 78:4507-4519. [PMID: 33884444 PMCID: PMC8195903 DOI: 10.1007/s00018-021-03797-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/19/2021] [Accepted: 02/19/2021] [Indexed: 11/10/2022]
Abstract
During early embryonic development both the rapid increase in cell number and the expression of genes that control developmental decisions are tightly regulated. Accumulating evidence has indicated that these two seemingly independent processes are mechanistically intertwined. The picture that emerges from studies on the cell cycle of embryonic stem cells is one in which proteins that promote cell cycle progression prevent differentiation and vice versa. Here, we review which transcription factors and signalling pathways play a role in both maintenance of pluripotency as well as cell cycle progression. We will not only describe the mechanism behind their function but also discuss the role of these regulators in different states of mouse pluripotency. Finally, we elaborate on how canonical cell cycle regulators impact on the molecular networks that control the maintenance of pluripotency and lineage specification.
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Affiliation(s)
- Menno Ter Huurne
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525GA, Nijmegen, The Netherlands
- Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Rd, Parkville, Melbourne, VIC, 3052, Australia
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525GA, Nijmegen, The Netherlands.
- Princess Maxima Centre for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands.
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12
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Lim S, Shparberg RA, Coorssen JR, O’Connor MD. Application of the RBBP9 Serine Hydrolase Inhibitor, ML114, Decouples Human Pluripotent Stem Cell Proliferation and Differentiation. Int J Mol Sci 2020; 21:ijms21238983. [PMID: 33256189 PMCID: PMC7730578 DOI: 10.3390/ijms21238983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/13/2020] [Accepted: 11/20/2020] [Indexed: 12/14/2022] Open
Abstract
Retinoblastoma binding protein 9 (RBBP9) is required for maintaining the expression of both pluripotency and cell cycle genes in human pluripotent stem cells (hPSCs). An siRNA-based study from our group showed it does so by influencing cell cycle progression through the RB/E2F pathway. In non-pluripotent cells, RBBP9 is also known to have serine hydrolase (SH) activity, acting on currently undefined target proteins. The role of RBBP9 SH activity in hPSCs, and during normal development, is currently unknown. To begin assessing whether RBBP9 SH activity might contribute to hPSC maintenance, hPSCs were treated with ML114—a selective chemical inhibitor of RBBP9 SH activity. Stem cells treated with ML114 showed significantly reduced population growth rate, colony size and progression through the cell cycle, with no observable change in cell morphology or decrease in pluripotency antigen expression—suggesting no initiation of hPSC differentiation. Consistent with this, hPSCs treated with ML114 retained the capacity for tri-lineage differentiation, as seen through teratoma formation. Subsequent microarray and Western blot analyses of ML114-treated hPSCs suggest the nuclear transcription factor Y subunit A (NFYA) may be a candidate effector of RBBP9 SH activity in hPSCs. These data support a role for RBBP9 in regulating hPSC proliferation independent of differentiation, whereby inhibition of RBBP9 SH activity de-couples decreased hPSC proliferation from initiation of differentiation.
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Affiliation(s)
- Seakcheng Lim
- School of Medicine, Western Sydney University, Campbelltown NSW 2560, Australia; (S.L.); (R.A.S.)
| | - Rachel A. Shparberg
- School of Medicine, Western Sydney University, Campbelltown NSW 2560, Australia; (S.L.); (R.A.S.)
| | - Jens R. Coorssen
- Departments of Health Sciences and Biological Sciences, Faculties of Applied Health Sciences and Mathematics & Science, Brock University, St. Catharines, ON L2S 3A1, Canada;
| | - Michael D. O’Connor
- School of Medicine, Western Sydney University, Campbelltown NSW 2560, Australia; (S.L.); (R.A.S.)
- Molecular Medicine Research Group, Western Sydney University, Campbelltown NSW 2560, Australia
- Correspondence:
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13
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Espinal-Centeno A, Dipp-Álvarez M, Saldaña C, Bako L, Cruz-Ramírez A. Conservation analysis of core cell cycle regulators and their transcriptional behavior during limb regeneration in Ambystoma mexicanum. Mech Dev 2020; 164:103651. [PMID: 33127453 DOI: 10.1016/j.mod.2020.103651] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 10/01/2020] [Accepted: 10/19/2020] [Indexed: 11/18/2022]
Abstract
Ambystoma mexicanum (axolotl) has been one of the major experimental models for the study of regeneration during the past 100 years. Axolotl limb regeneration takes place through a multi-stage and complex developmental process called epimorphosis that involves diverse events of cell reprogramming. Such events start with dedifferentiation of somatic cells and the proliferation of quiescent stem cells to generate a population of proliferative cells called blastema. Once the blastema reaches a mature stage, cells undergo progressive differentiation into the diverse cell lineages that will form the new limb. Such pivotal cell reprogramming phenomena depend on the fine-tuned regulation of the cell cycle in each regeneration stage, where cell populations display specific proliferative capacities and differentiation status. The axolotl genome has been fully sequenced and released recently, and diverse RNA-seq approaches have also been generated, enabling the identification and conservatory analysis of core cell cycle regulators in this species. We report here our results from such analyses and present the transcriptional behavior of key regulatory factors during axolotl limb regeneration. We also found conserved protein interactions between axolotl Cyclin Dependent Kinases 2, 4 and 6 and Cyclins type D and E. Canonical CYC-CDK interactions that play major roles in modulating cell cycle progression in eukaryotes.
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Affiliation(s)
- Annie Espinal-Centeno
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada (U.G.A.-LANGEBIO) CINVESTAV, Irapuato, Mexico; Facultad de Ciencias Naturales, Campus Juriquilla, Universidad Autónoma de Querétaro, Av. de las Ciencias S/N, Juriquilla, Querétaro, Qro. CP 76230, Mexico
| | - Melissa Dipp-Álvarez
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada (U.G.A.-LANGEBIO) CINVESTAV, Irapuato, Mexico
| | - Carlos Saldaña
- Facultad de Ciencias Naturales, Campus Juriquilla, Universidad Autónoma de Querétaro, Av. de las Ciencias S/N, Juriquilla, Querétaro, Qro. CP 76230, Mexico
| | - Laszlo Bako
- Department of Plant Physiology, Umeå University, Umeå, Sweden.
| | - Alfredo Cruz-Ramírez
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada (U.G.A.-LANGEBIO) CINVESTAV, Irapuato, Mexico.
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14
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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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15
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Wragg JW, Roos L, Vucenovic D, Cvetesic N, Lenhard B, Müller F. Embryonic tissue differentiation is characterized by transitions in cell cycle dynamic-associated core promoter regulation. Nucleic Acids Res 2020; 48:8374-8392. [PMID: 32619237 PMCID: PMC7470974 DOI: 10.1093/nar/gkaa563] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 06/10/2020] [Accepted: 06/19/2020] [Indexed: 12/30/2022] Open
Abstract
The core-promoter, a stretch of DNA surrounding the transcription start site (TSS), is a major integration-point for regulatory-signals controlling gene-transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell-cycling behaviour between cells of different fates. The role promoter-associated gene-regulatory-networks play in development-associated transitions in cell-cycle-dynamics is poorly understood. This study demonstrates in a vertebrate embryo, how core-promoter variations define transcriptional output in cells transitioning from a proliferative to cell-lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo segmentation, using the FUCCI transgenic cell-cycle-phase marker, revealed a spatial and lineage-specific separation in cell-cycling behaviour. To investigate the role differential promoter usage plays in this process, cap-analysis-of-gene-expression (CAGE) was performed on cells segregated by cycling dynamics. This analysis revealed a dramatic increase in tissue-specific gene expression, concurrent with slowed cycling behaviour. We revealed a distinct sharpening in TSS utilization in genes upregulated in slowly cycling, differentiating tissues, associated with enhanced utilization of the TATA-box, in addition to Sp1 binding-sites. In contrast, genes upregulated in rapidly cycling cells carry broad distribution of TSS utilization, coupled with enrichment for the CCAAT-box. These promoter features appear to correspond to cell-cycle-dynamic rather than tissue/cell-lineage origin. Moreover, we observed genes with cell-cycle-dynamic-associated transitioning in TSS distribution and differential utilization of alternative promoters. These results demonstrate the regulatory role of core-promoters in cell-cycle-dependent transcription regulation, during embryo-development.
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Affiliation(s)
| | | | - Dunja Vucenovic
- Institute of Clinical Sciences and MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Nevena Cvetesic
- Institute of Clinical Sciences and MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Boris Lenhard
- Correspondence may also be addressed to Boris Lenhard. Tel: +44 20 3313 8353;
| | - Ferenc Müller
- To whom correspondence should be addressed. Tel: +44 121 414 2895;
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16
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Maintenance of genome integrity and active homologous recombination in embryonic stem cells. Exp Mol Med 2020; 52:1220-1229. [PMID: 32770082 PMCID: PMC8080833 DOI: 10.1038/s12276-020-0481-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/12/2020] [Accepted: 06/23/2020] [Indexed: 12/11/2022] Open
Abstract
Embryonic stem cells (ESCs) possess specific gene expression patterns that confer the ability to proliferate indefinitely and enable pluripotency, which allows ESCs to differentiate into diverse cell types in response to developmental signals. Compared to differentiated cells, ESCs harbor an elevated level of homologous recombination (HR)-related proteins and exhibit exceptional cell cycle control, characterized by a high proliferation rate and a prolonged S phase. HR is involved in several aspects of chromosome maintenance. For instance, HR repairs impaired chromosomes and prevents the collapse of DNA replication forks during cell proliferation. Thus, HR is essential for the maintenance of genomic integrity and prevents cellular dysregulation and lethal events. In addition, abundant HR proteins in the prolonged S phase can efficiently protect ESCs from external damages and protect against genomic instability caused by DNA breaks, facilitating rapid and accurate DNA break repair following chromosome duplication. The maintenance of genome integrity is key to preserving the functions of ESCs and reducing the risks of cancer development, cell cycle arrest, and abnormal replication. Here, we review the fundamental links between the stem cell-specific HR process and DNA damage response as well as the different strategies employed by ESCs to maintain genomic integrity. Embryonic stem cells (ESCs), which give rise to the many specialized cells of the body, have highly effective molecular processes of DNA maintenance and repair which protect their genetic information from damage. Keun Pil Kim and colleagues at Chung-Ang University, Seoul, South Korea, review the strategies found in ESCs to maintain the integrity of their DNA as they develop and multiply. A key feature is the process of homologous recombination (HR) in which one copy of a section of DNA acts as the template allowing a damaged version of the DNA to be repaired. HR also facilitates swapping of sections of DNA when sperm and egg cells form, promoting genetic diversity. HR appears to be especially significant in maintaining ESC DNA as ESCs possess higher levels of key proteins involved in its maintenance and regulation.
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17
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Yang J, Jiang W. The Role of SMAD2/3 in Human Embryonic Stem Cells. Front Cell Dev Biol 2020; 8:653. [PMID: 32850796 PMCID: PMC7396709 DOI: 10.3389/fcell.2020.00653] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/01/2020] [Indexed: 12/11/2022] Open
Abstract
Human embryonic stem cells (hESCs) possess the potential of long-term self-renewal and three primary germ layers differentiation, and thus hESCs are expected to have broad applications in cell therapy, drug screening and basic research on human early embryonic development. Many efforts have been put to dissect the regulation of pluripotency and direct differentiation of hESCs. TGFβ/Activin/Nodal signal pathway critically regulates pluripotency maintenance and cell differentiation through the main signal transducer SMAD2/3 in hESCs, but the action manners of SMAD2/3 in hESCs are sophisticated and not documented yet. Here we review and discuss the roles of SMAD2/3 in hESC pluripotency maintenance and differentiation initiation separately. We summarize that SMAD2/3 regulates pluripotency and differentiation mainly through four aspects, (1) controlling divergent transcriptional networks of pluripotency and differentiation; (2) interacting with chromatin modifiers to make the chromatin accessible or recruiting METTL3-METTL14-WTAP complex and depositing m6A to the mRNA of pluripotency genes; (3) acting as a transcription factor to activate endoderm-specific genes to thus initiate definitive endoderm differentiation, which happens as cyclin D/CDK4/6 downstream target in later G1 phase as well; (4) interacting with endoderm specific lncRNAs to promote differentiation.
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Affiliation(s)
- Jie Yang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Wei Jiang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China.,Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan University, Wuhan, China.,Human Genetics Resource Preservation Center of Wuhan University, Wuhan, China
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18
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Padgett J, Santos SDM. From clocks to dominoes: lessons on cell cycle remodelling from embryonic stem cells. FEBS Lett 2020; 594:2031-2045. [PMID: 32535913 DOI: 10.1002/1873-3468.13862] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 05/01/2020] [Accepted: 05/27/2020] [Indexed: 12/21/2022]
Abstract
Cell division is a fundamental cellular process and the evolutionarily conserved networks that control cell division cycles adapt during development, tissue regeneration, cell de-differentiation and reprogramming, and a variety of pathological conditions. Embryonic development is a prime example of such versatility: fast, clock-like divisions hallmarking embryonic cells at early developmental stages become slower and controlled during cellular differentiation and lineage specification. In this review, we compare and contrast the unique cell cycle of mouse and human embryonic stem cells with that of early embryonic cells and of differentiated cells. We propose that embryonic stem cells provide an extraordinarily useful model system to understand cell cycle remodelling during embryonic-to-somatic transitions. We discuss how cell cycle networks help sustain embryonic stem cell pluripotency and self-renewal and how they safeguard cell identity and proper cell number in differentiated cells. Finally, we highlight the incredible diversity in cell cycle regulation within mammals and discuss the implications of studying cell cycle remodelling for understanding healthy and disease states.
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Affiliation(s)
- Joe Padgett
- Quantitative Cell Biology Lab, The Francis Crick Institute, London, UK
| | - Silvia D M Santos
- Quantitative Cell Biology Lab, The Francis Crick Institute, London, UK
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19
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Lau KX, Mason EA, Kie J, De Souza DP, Kloehn J, Tull D, McConville MJ, Keniry A, Beck T, Blewitt ME, Ritchie ME, Naik SH, Zalcenstein D, Korn O, Su S, Romero IG, Spruce C, Baker CL, McGarr TC, Wells CA, Pera MF. Unique properties of a subset of human pluripotent stem cells with high capacity for self-renewal. Nat Commun 2020; 11:2420. [PMID: 32415101 PMCID: PMC7229198 DOI: 10.1038/s41467-020-16214-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 04/16/2020] [Indexed: 01/06/2023] Open
Abstract
Archetypal human pluripotent stem cells (hPSC) are widely considered to be equivalent in developmental status to mouse epiblast stem cells, which correspond to pluripotent cells at a late post-implantation stage of embryogenesis. Heterogeneity within hPSC cultures complicates this interspecies comparison. Here we show that a subpopulation of archetypal hPSC enriched for high self-renewal capacity (ESR) has distinct properties relative to the bulk of the population, including a cell cycle with a very low G1 fraction and a metabolomic profile that reflects a combination of oxidative phosphorylation and glycolysis. ESR cells are pluripotent and capable of differentiation into primordial germ cell-like cells. Global DNA methylation levels in the ESR subpopulation are lower than those in mouse epiblast stem cells. Chromatin accessibility analysis revealed a unique set of open chromatin sites in ESR cells. RNA-seq at the subpopulation and single cell levels shows that, unlike mouse epiblast stem cells, the ESR subset of hPSC displays no lineage priming, and that it can be clearly distinguished from gastrulating and extraembryonic cell populations in the primate embryo. ESR hPSC correspond to an earlier stage of post-implantation development than mouse epiblast stem cells. Human pluripotent cells (hPSCs) in standard culture are similar to mouse epiblast cells, but heterogeneity within hPSC cultures complicates comparisons. Here the authors show that a subpopulation of hPSCs enriched for self-renewal capacity have distinct cell cycle, metabolic, DNA methylation, and ATAC-seq profiles.
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Affiliation(s)
- Kevin X Lau
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Elizabeth A Mason
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Joshua Kie
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - David P De Souza
- Metabolomics Australia, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Joachim Kloehn
- Department of Biochemistry and Molecular Biology, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Dedreia Tull
- Metabolomics Australia, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Malcolm J McConville
- Metabolomics Australia, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, 3052, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Andrew Keniry
- Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Tamara Beck
- Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia
| | - Marnie E Blewitt
- Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Matthew E Ritchie
- Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia
| | - Shalin H Naik
- Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia
| | - Daniela Zalcenstein
- Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia
| | - Othmar Korn
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Shian Su
- Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia
| | - Irene Gallego Romero
- Melbourne Integrative Genomics, School of Biosciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | | | | | | | - Christine A Wells
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, 3010, Australia.,Divisions of Cancer and Hematology and Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia
| | - Martin F Pera
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Victoria, 3010, Australia. .,Division of Molecular Medicine, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3052, Australia. .,The Jackson Laboratory, Bar Harbor, ME, 04609, USA. .,The Florey Institute of Neuroscience and Mental Health, 30 Royal Parade, Parkville, Victoria, 3052, Australia.
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20
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Afanassieff M, Perold F, Bouchereau W, Cadiou A, Beaujean N. Embryo-derived and induced pluripotent stem cells: Towards naive pluripotency and chimeric competency in rabbits. Exp Cell Res 2020; 389:111908. [PMID: 32057751 DOI: 10.1016/j.yexcr.2020.111908] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/08/2020] [Accepted: 02/10/2020] [Indexed: 12/17/2022]
Abstract
Both embryo-derived (ESC) and induced pluripotent stem cell (iPSC) lines have been established in rabbit. They exhibit the essential characteristics of primed pluripotency. In this review, we described their characteristic features at both molecular and functional levels. We also described the attempts to reprogram rabbit pluripotent stem cells (rbPSCs) toward the naive state of pluripotency using methods established previously to capture this state in rodents and primates. In the last section, we described and discussed our current knowledge of rabbit embryo development pertaining to the mechanisms of early lineage segregation. We argued that the molecular signature of naive-state pluripotency differs between mice and rabbits. We finally discussed some of the key issues to be addressed for capturing the naive state in rbPSCs, including the generation of embryo/PSC chimeras.
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Affiliation(s)
- Marielle Afanassieff
- Univ Lyon, Université Lyon 1, Inserm, INRAE, Stem Cell and Brain Research Institute, U1208, USC1361, F-69500, Bron, France.
| | - Florence Perold
- Univ Lyon, Université Lyon 1, Inserm, INRAE, Stem Cell and Brain Research Institute, U1208, USC1361, F-69500, Bron, France
| | - Wilhelm Bouchereau
- Univ Lyon, Université Lyon 1, Inserm, INRAE, Stem Cell and Brain Research Institute, U1208, USC1361, F-69500, Bron, France
| | - Antoine Cadiou
- Univ Lyon, Université Lyon 1, Inserm, INRAE, Stem Cell and Brain Research Institute, U1208, USC1361, F-69500, Bron, France
| | - Nathalie Beaujean
- Univ Lyon, Université Lyon 1, Inserm, INRAE, Stem Cell and Brain Research Institute, U1208, USC1361, F-69500, Bron, France
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21
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The cell cycle in stem cell proliferation, pluripotency and differentiation. Nat Cell Biol 2019; 21:1060-1067. [PMID: 31481793 DOI: 10.1038/s41556-019-0384-4] [Citation(s) in RCA: 180] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 07/24/2019] [Indexed: 12/30/2022]
Abstract
Cyclins, cyclin-dependent kinases and other components of the core cell cycle machinery drive cell division. Growing evidence indicates that this machinery operates in a distinct fashion in some mammalian stem cell types, such as pluripotent embryonic stem cells. In this Review, we discuss our current knowledge of how cell cycle proteins mechanistically link cell proliferation, pluripotency and cell fate specification. We focus on embryonic stem cells, induced pluripotent stem cells and embryonic neural stem/progenitor cells.
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22
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Videla-Richardson GA, Furmento VA, Garcia CP, Morris-Hanon O, Sevlever GE, Romorini L, Scassa ME. Human embryonic stem cells display a pronounced sensitivity to the cyclin dependent kinase inhibitor Roscovitine. BMC Mol Cell Biol 2019; 20:40. [PMID: 31462218 PMCID: PMC6712821 DOI: 10.1186/s12860-019-0222-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 08/19/2019] [Indexed: 12/14/2022] Open
Abstract
Background The essentially unlimited expansion potential and the pluripotency of human embryonic stem cells (hESCs) make them attractive for cell-based therapeutic purposes. Although hESCs can indefinitely proliferate in culture, unlike transformed cancer cells, they are endowed with a cell-intrinsic property termed mitochondrial priming that renders them highly sensitive to apoptotic stimuli. Thus, all attempts to broaden the insights into hESCs apoptosis may be helpful for establishing pro-survival strategies valuable for its in vitro culture and further use in clinical applications. Cyclin-dependent kinases (CDKs), a family of serine/threonine protein kinases originally identified as regulators of the eukaryotic cell cycle, can also regulate transcription and differentiation. Moreover, there are compelling data suggesting that its activities are involved in certain apoptotic programs in different cell types. Currently, it is not completely determined whether CDKs regulate apoptotic processes in rapidly proliferating and apoptosis-prone hESCs. In this study, to elucidate the effect of CDKs inhibition in hESCs we used Roscovitine (ROSC), a purine analogue that selectively inhibits the activities of these kinases. Results Inhibition of CDKs by ROSC triggers programmed cell death in hESCs but not in proliferating somatic cells (human fibroblasts). The apoptotic process encompasses caspase-9 and -3 activation followed by PARP cleavage. ROSC treatment also leads to p53 stabilization, which coincides with site-specific phosphorylation at serine 46 and decreased levels of Mdm2. Additionally, we observed a transcriptional induction of p53AIP1, a repression of pro-survival factor Mcl-1 and an up-regulation of pro-apoptotic BH3-only proteins NOXA and PUMA. Importantly, we found that the role of CDK2 inhibition appears to be at best accessory as an active CDK2 is not required to ensure hESCs survival. Conclusion Our experimental data reveal that hESCs, contrary to fibroblasts, exhibit a pronounced sensitivity to ROSC.
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Affiliation(s)
- Guillermo A Videla-Richardson
- Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET), Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (FLENI), Belén de Escobar, Provincia de Buenos Aires, Argentina
| | - Verónica A Furmento
- Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET), Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (FLENI), Belén de Escobar, Provincia de Buenos Aires, Argentina
| | - Carolina P Garcia
- Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET), Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (FLENI), Belén de Escobar, Provincia de Buenos Aires, Argentina
| | - Olivia Morris-Hanon
- Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET), Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (FLENI), Belén de Escobar, Provincia de Buenos Aires, Argentina
| | - Gustavo E Sevlever
- Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET), Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (FLENI), Belén de Escobar, Provincia de Buenos Aires, Argentina
| | - Leonardo Romorini
- Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET), Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (FLENI), Belén de Escobar, Provincia de Buenos Aires, Argentina
| | - María E Scassa
- Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET), Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (FLENI), Belén de Escobar, Provincia de Buenos Aires, Argentina.
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23
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Rodríguez Varela MS, Mucci S, Videla Richardson GA, Morris Hanon O, Furmento VA, Miriuka SG, Sevlever GE, Scassa ME, Romorini L. Regulation of cyclin E1 expression in human pluripotent stem cells and derived neural progeny. Cell Cycle 2018; 17:1721-1744. [PMID: 29995582 DOI: 10.1080/15384101.2018.1496740] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Human pluripotent stem cells (hPSCs), including embryonic and induced pluripotent stem cells (hESCs and hiPSCs) show unique cell cycle characteristics, such as a short doubling time due to an abbreviated G1 phase. Whether or not the core cell cycle machinery directly regulates the stemness and/or the differentiation potential of hPSCs remains to be determined. To date, several scenarios describing the atypical cell cycle of hPSCs have been suggested, and therefore there is still controversy over how cyclins, master regulators of the cell cycle, are expressed and regulated. Furthermore, the cell cycle profile and the expression pattern of major cyclins in hESCs-derived neuroprogenitors (NP) have not been studied yet. Therefore, herein we characterized the expression pattern of major cyclins in hPSCs and NP. We determined that all studied cyclins mRNA expression levels fluctuate along cell cycle. Particularly, after a thorough analysis of synchronized cell populations, we observed that cyclin E1 mRNA levels increased sharply in G1/S concomitantly with cyclin E1 protein accumulation in hPSCs and NP. Additionally, we demonstrated that cyclin E1 mRNA expression levels involves the activation of MEK/ERK pathway and the transcription factors c-Myc and E2Fs in hPSCs. Lastly, our results reveal that proteasome mediates the marked down-regulation (degradation) of cyclin E1 protein observed in G2/M by a mechanism that requires a functional CDK2 but not GSK3β activity. ABBREVIATIONS hPSCs: human pluripotent stem cells; hESCs: human embryonic stem cells; hiPSCs: human induced pluripotent stem cells; NP: neuroprogenitors; HF: human foreskin fibroblasts; MEFs: mouse embryonic fibroblasts; iMEFs: irradiated mouse embryonic fibroblasts; CDKs: cyclindependent kinases; CKIs: CDK inhibitors; CNS: central nervous system; Oct-4: Octamer-4; EB: embryoid body; AFP: Alpha-fetoprotein; cTnT: Cardiac Troponin T; MAP-2: microtubule-associated protein; TUJ-1: neuron-specific class III β-tubulin; bFGF: basic fibroblastic growth factor; PI3K: Phosphoinositide 3-kinase; KSR: knock out serum replacement; CM: iMEF conditioned medium; E8: Essential E8 medium.
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Affiliation(s)
- María Soledad Rodríguez Varela
- a Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET) , Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (FLENI) , Belén de Escobar , Provincia de Buenos Aires , Argentina
| | - Sofía Mucci
- a Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET) , Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (FLENI) , Belén de Escobar , Provincia de Buenos Aires , Argentina
| | - Guillermo Agustín Videla Richardson
- a Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET) , Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (FLENI) , Belén de Escobar , Provincia de Buenos Aires , Argentina
| | - Olivia Morris Hanon
- a Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET) , Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (FLENI) , Belén de Escobar , Provincia de Buenos Aires , Argentina
| | - Verónica Alejandra Furmento
- a Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET) , Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (FLENI) , Belén de Escobar , Provincia de Buenos Aires , Argentina
| | - Santiago Gabriel Miriuka
- a Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET) , Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (FLENI) , Belén de Escobar , Provincia de Buenos Aires , Argentina
| | - Gustavo Emilio Sevlever
- a Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET) , Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (FLENI) , Belén de Escobar , Provincia de Buenos Aires , Argentina
| | - María Elida Scassa
- a Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET) , Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (FLENI) , Belén de Escobar , Provincia de Buenos Aires , Argentina
| | - Leonardo Romorini
- a Laboratorios de Investigación Aplicada en Neurociencias (LIAN-CONICET) , Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (FLENI) , Belén de Escobar , Provincia de Buenos Aires , Argentina
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24
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Zaveri L, Dhawan J. Cycling to Meet Fate: Connecting Pluripotency to the Cell Cycle. Front Cell Dev Biol 2018; 6:57. [PMID: 29974052 PMCID: PMC6020794 DOI: 10.3389/fcell.2018.00057] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 05/14/2018] [Indexed: 01/26/2023] Open
Abstract
Pluripotent stem cells are characterized by their high proliferative rates, their ability to self-renew and their potential to differentiate to all the three germ layers. This rapid proliferation is brought about by a highly modified cell cycle that allows the cells to quickly shuttle from DNA synthesis to cell division, by reducing the time spent in the intervening gap phases. Many key regulators that define the somatic cell cycle are either absent or exhibit altered behavior, allowing the pluripotent cell to bypass cell cycle checkpoints typical of somatic cells. Experimental analysis of this modified stem cell cycle has been challenging due to the strong link between rapid proliferation and pluripotency, since perturbations to the cell cycle or pluripotency factors result in differentiation. Despite these hurdles, our understanding of this unique cell cycle has greatly improved over the past decade, in part because of the availability of new technologies that permit the analysis of single cells in heterogeneous populations. This review aims to highlight some of the recent discoveries in this area with a special emphasis on different states of pluripotency. We also discuss the highly interlinked network that connects pluripotency factors and key cell cycle genes and review evidence for how this interdependency may promote the rapid cell cycle. This issue gains translational importance since disruptions in stem cell proliferation and differentiation can impact disorders at opposite ends of a spectrum, from cancer to degenerative disease.
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Affiliation(s)
- Lamuk Zaveri
- Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, India.,CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India.,Manipal Academy of Higher Education, Manipal, India
| | - Jyotsna Dhawan
- Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, India.,CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India
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25
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Rasmussen ML, Ortolano NA, Romero-Morales AI, Gama V. Wnt Signaling and Its Impact on Mitochondrial and Cell Cycle Dynamics in Pluripotent Stem Cells. Genes (Basel) 2018; 9:genes9020109. [PMID: 29463061 PMCID: PMC5852605 DOI: 10.3390/genes9020109] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/13/2018] [Accepted: 02/14/2018] [Indexed: 12/17/2022] Open
Abstract
The core transcriptional network regulating stem cell self-renewal and pluripotency remains an intense area of research. Increasing evidence indicates that modified regulation of basic cellular processes such as mitochondrial dynamics, apoptosis, and cell cycle are also essential for pluripotent stem cell identity and fate decisions. Here, we review evidence for Wnt regulation of pluripotency and self-renewal, and its connections to emerging features of pluripotent stem cells, including (1) increased mitochondrial fragmentation, (2) increased sensitivity to cell death, and (3) shortened cell cycle. We provide a general overview of the stem cell–specific mechanisms involved in the maintenance of these uncharacterized hallmarks of pluripotency and highlight potential links to the Wnt signaling pathway. Given the physiological importance of stem cells and their enormous potential for regenerative medicine, understanding fundamental mechanisms mediating the crosstalk between Wnt, organelle-dynamics, apoptosis, and cell cycle will be crucial to gain insight into the regulation of stemness.
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Affiliation(s)
- Megan L Rasmussen
- Department of Cell and Developmental Biology; Vanderbilt University, Nashville, TN37232, United States.
| | - Natalya A Ortolano
- Department of Cell and Developmental Biology; Vanderbilt University, Nashville, TN37232, United States.
| | | | - Vivian Gama
- Department of Cell and Developmental Biology; Vanderbilt University, Nashville, TN37232, United States.
- Vanderbilt Center for Stem Cell Biology; Vanderbilt University, Nashville, TN37232, United States.
- Vanderbilt Ingram Cancer Center; Vanderbilt University, Nashville, TN37232, United States.
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26
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Salz HK, Dawson EP, Heaney JD. Germ cell tumors: Insights from the Drosophila ovary and the mouse testis. Mol Reprod Dev 2017; 84:200-211. [PMID: 28079292 DOI: 10.1002/mrd.22779] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 01/10/2017] [Indexed: 12/14/2022]
Abstract
Ovarian and testicular germ cell tumors of young adults are thought to arise from defects in germ cell development, but the molecular mechanisms underlying malignant transformation are poorly understood. In this review, we focus on the biology of germ cell tumor formation in the Drosophila ovary and the mouse testis, for which evidence supports common underlying mechanisms, such as blocking initiation into the differentiation pathway, impaired lineage progression, and sexual identity instability. We then discuss how these concepts inform our understanding of the disease in humans. Mol. Reprod. Dev. 84: 200-211, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Helen K Salz
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Emily P Dawson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Jason D Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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27
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Matson JP, Dumitru R, Coryell P, Baxley RM, Chen W, Twaroski K, Webber BR, Tolar J, Bielinsky AK, Purvis JE, Cook JG. Rapid DNA replication origin licensing protects stem cell pluripotency. eLife 2017; 6:30473. [PMID: 29148972 PMCID: PMC5720591 DOI: 10.7554/elife.30473] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 11/16/2017] [Indexed: 11/24/2022] Open
Abstract
Complete and robust human genome duplication requires loading minichromosome maintenance (MCM) helicase complexes at many DNA replication origins, an essential process termed origin licensing. Licensing is restricted to G1 phase of the cell cycle, but G1 length varies widely among cell types. Using quantitative single-cell analyses, we found that pluripotent stem cells with naturally short G1 phases load MCM much faster than their isogenic differentiated counterparts with long G1 phases. During the earliest stages of differentiation toward all lineages, MCM loading slows concurrently with G1 lengthening, revealing developmental control of MCM loading. In contrast, ectopic Cyclin E overproduction uncouples short G1 from fast MCM loading. Rapid licensing in stem cells is caused by accumulation of the MCM loading protein, Cdt1. Prematurely slowing MCM loading in pluripotent cells not only lengthens G1 but also accelerates differentiation. Thus, rapid origin licensing is an intrinsic characteristic of stem cells that contributes to pluripotency maintenance. From red blood cells to nerve cells, animals’ bodies contain many different types of specialized cells. These all begin as stem cells, which have the potential to divide and make more stem cells or to specialize. All dividing cells must first unwind their DNA so that it can be copied. To achieve this, cells load DNA-unwinding enzymes called helicases onto their DNA during the part of the cell cycle known as G1 phase. Cells must load enough helicase enzymes to ensure that their DNA is copied completely and in time. Stem cells divide faster than their specialized descendants, and have a much shorter G1 phase too. Yet these cells still manage to load enough helicases to copy their DNA. Little is known about how the amount, rate and timing of helicase loading varies between cells that divide at different speeds. Now Matson et al. have measured how quickly helicase enzymes are loaded onto DNA in individual human cells, including stem cells and specialized or “differentiated” cells. Stem cells loaded helicases rapidly to make up for the short time they spent in G1 phase, while differentiated cells loaded the enzymes more slowly. Measuring how the loading rate changed when stem cells were triggered to specialize showed that helicase loading slowed as the G1 phase got longer. Matson et al. found that the levels of key proteins required for helicase loading correlated with the rates of loading. Altering the levels of the proteins changed how quickly the enzymes were loaded and how the cells behaved – for example, slowing down the loading of helicases made the stem cells specialize quicker. These findings show that the processes of cell differentiation and DNA replication are closely linked. This study and future ones will help scientists understand what is happening during early animal development, when specialization first takes place, as well as what has gone wrong in cancer cells, which also divide quickly. A better understanding of this process also helps in regenerative medicine – where one of the challenges is to make enough specialized cells to transplant into a patient with tissue damage without those cells becoming cancerous.
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Affiliation(s)
- Jacob Peter Matson
- Department of Biochemistry and Biophysics, The University of North Carolina, Chapel Hill, United States
| | - Raluca Dumitru
- Human Pluripotent Stem Cell Core Facility, The University of North Carolina, Chapel Hill, United States
| | - Philip Coryell
- Department of Genetics, The University of North Carolina, Chapel Hill, United States
| | - Ryan M Baxley
- Department of Biochemistry, Molecular Biology, and Biophysics, The University of Minnesota, Minneapolis, United States
| | - Weili Chen
- Stem Cell Institute, University of Minnesota, Minnesota, United States
| | - Kirk Twaroski
- Stem Cell Institute, University of Minnesota, Minnesota, United States
| | - Beau R Webber
- Stem Cell Institute, University of Minnesota, Minnesota, United States
| | - Jakub Tolar
- Stem Cell Institute, University of Minnesota, Minnesota, United States
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology, and Biophysics, The University of Minnesota, Minneapolis, United States
| | - Jeremy E Purvis
- Department of Genetics, The University of North Carolina, Chapel Hill, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, United States
| | - Jeanette Gowen Cook
- Department of Biochemistry and Biophysics, The University of North Carolina, Chapel Hill, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, United States
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28
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She S, Wei Q, Kang B, Wang YJ. Cell cycle and pluripotency: Convergence on octamer‑binding transcription factor 4 (Review). Mol Med Rep 2017; 16:6459-6466. [PMID: 28901500 PMCID: PMC5865814 DOI: 10.3892/mmr.2017.7489] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 07/14/2017] [Indexed: 12/14/2022] Open
Abstract
Embryonic stem cells (ESCs) have unlimited expansion potential and the ability to differentiate into all somatic cell types for regenerative medicine and disease model studies. Octamer-binding transcription factor 4 (OCT4), encoded by the POU domain, class 5, transcription factor 1 gene, is a transcription factor vital for maintaining ESC pluripotency and somatic reprogramming. Many studies have established that the cell cycle of ESCs is featured with an abbreviated G1 phase and a prolonged S phase. Changes in cell cycle dynamics are intimately associated with the state of ESC pluripotency, and manipulating cell-cycle regulators could enable a controlled differentiation of ESCs. The present review focused primarily on the emerging roles of OCT4 in coordinating the cell cycle progression, the maintenance of pluripotency and the glycolytic metabolism in ESCs.
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Affiliation(s)
- Shiqi She
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Qucheng Wei
- Cardiovascular Key Lab of Zhejiang, Department of Cardiology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310009, P.R. China
| | - Bo Kang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Ying-Jie Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
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29
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Waisman A, Vazquez Echegaray C, Solari C, Cosentino MS, Martyn I, Deglincerti A, Ozair MZ, Ruzo A, Barañao L, Miriuka S, Brivanlou A, Guberman A. Inhibition of Cell Division and DNA Replication Impair Mouse-Naïve Pluripotency Exit. J Mol Biol 2017; 429:2802-2815. [PMID: 28684247 DOI: 10.1016/j.jmb.2017.06.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 06/24/2017] [Accepted: 06/28/2017] [Indexed: 12/27/2022]
Abstract
The cell cycle has gained attention as a key determinant for cell fate decisions, but the contribution of DNA replication and mitosis in stem cell differentiation has not been extensively studied. To understand if these processes act as "windows of opportunity" for changes in cell identity, we established synchronized cultures of mouse embryonic stem cells as they exit the ground state of pluripotency. We show that initial transcriptional changes in this transition do not require passage through mitosis and that conversion to primed pluripotency is linked to lineage priming in the G1 phase. Importantly, we demonstrate that impairment of DNA replication severely blocks transcriptional switch to primed pluripotency, even in the absence of p53 activity induced by the DNA damage response. Our data suggest an important role for DNA replication during mouse embryonic stem cell differentiation, which could shed light on why pluripotent cells are only receptive to differentiation signals during G1, that is, before the S phase.
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Affiliation(s)
- Ariel Waisman
- Universidad de Buenos Aires, Laboratorio de Regulación Génica en Células Madre, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Química Biológica (IQUIBICEN), Buenos Aires, Argentina
| | - Camila Vazquez Echegaray
- Universidad de Buenos Aires, Laboratorio de Regulación Génica en Células Madre, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Química Biológica (IQUIBICEN), Buenos Aires, Argentina
| | - Claudia Solari
- Universidad de Buenos Aires, Laboratorio de Regulación Génica en Células Madre, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Química Biológica (IQUIBICEN), Buenos Aires, Argentina
| | - María Soledad Cosentino
- Universidad de Buenos Aires, Laboratorio de Regulación Génica en Células Madre, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Química Biológica (IQUIBICEN), Buenos Aires, Argentina
| | - Iain Martyn
- Laboratory of Stem Cell Biology and Molecular Embryology, The Rockefeller University, New York, NY 10065, USA
| | - Alessia Deglincerti
- Laboratory of Stem Cell Biology and Molecular Embryology, The Rockefeller University, New York, NY 10065, USA
| | - Mohammad Zeeshan Ozair
- Laboratory of Stem Cell Biology and Molecular Embryology, The Rockefeller University, New York, NY 10065, USA
| | - Albert Ruzo
- Laboratory of Stem Cell Biology and Molecular Embryology, The Rockefeller University, New York, NY 10065, USA
| | - Lino Barañao
- Universidad de Buenos Aires, Laboratorio de Regulación Génica en Células Madre, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Santiago Miriuka
- CONICET-Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia (FLENI), Laboratorio de Investigación de Aplicación a Neurociencias (LIAN), Buenos Aires, Argentina
| | - Ali Brivanlou
- Laboratory of Stem Cell Biology and Molecular Embryology, The Rockefeller University, New York, NY 10065, USA
| | - Alejandra Guberman
- Universidad de Buenos Aires, Laboratorio de Regulación Génica en Células Madre, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Química Biológica (IQUIBICEN), Buenos Aires, Argentina; Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
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30
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Structure of Nascent Chromatin Is Essential for Hematopoietic Lineage Specification. Cell Rep 2017; 19:295-306. [PMID: 28402853 DOI: 10.1016/j.celrep.2017.03.035] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 12/28/2016] [Accepted: 03/09/2017] [Indexed: 12/12/2022] Open
Abstract
The role of chromatin structure in lineage commitment of multipotent hematopoietic progenitors (HPCs) is presently unclear. We show here that CD34+ HPCs possess a post-replicative chromatin globally devoid of the repressive histone mark H3K27me3. This H3K27-unmodified chromatin is required for recruitment of lineage-determining transcription factors (TFs) C/EBPα, PU.1, and GATA-1 to DNA just after DNA replication upon cytokine-induced myeloid or erythroid commitment. Blocking DNA replication or increasing H3K27me3 levels prevents recruitment of these TFs to DNA and suppresses cytokine-induced erythroid or myeloid differentiation. However, H3K27me3 is rapidly associated with nascent DNA in more primitive human and murine HPCs. Treatment of these cells with instructive cytokines leads to a significant delay in accumulation of H3K27me3 in nascent chromatin due to activity of the H3K27me3 demethylase UTX. Thus, HPCs utilize special mechanisms of chromatin modification for recruitment of specific TFs to DNA during early stages of lineage specification.
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31
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Petruk S, Cai J, Sussman R, Sun G, Kovermann SK, Mariani SA, Calabretta B, McMahon SB, Brock HW, Iacovitti L, Mazo A. Delayed Accumulation of H3K27me3 on Nascent DNA Is Essential for Recruitment of Transcription Factors at Early Stages of Stem Cell Differentiation. Mol Cell 2017; 66:247-257.e5. [PMID: 28410996 DOI: 10.1016/j.molcel.2017.03.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 12/28/2016] [Accepted: 03/07/2017] [Indexed: 02/06/2023]
Abstract
Recruitment of transcription factors (TFs) to repressed genes in euchromatin is essential to activate new transcriptional programs during cell differentiation. However, recruitment of all TFs, including pioneer factors, is impeded by condensed H3K27me3-containing chromatin. Single-cell and gene-specific analyses revealed that, during the first hours of induction of differentiation of mammalian embryonic stem cells (ESCs), accumulation of the repressive histone mark H3K27me3 is delayed after DNA replication, indicative of a decondensed chromatin structure in all regions of the replicating genome. This delay provides a critical "window of opportunity" for recruitment of lineage-specific TFs to DNA. Increasing the levels of post-replicative H3K27me3 or preventing S phase entry inhibited recruitment of new TFs to DNA and significantly blocked cell differentiation. These findings suggest that recruitment of lineage-specifying TFs occurs soon after replication and is facilitated by a decondensed chromatin structure. This insight may explain the developmental plasticity of stem cells and facilitate their exploitation for therapeutic purposes.
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Affiliation(s)
- Svetlana Petruk
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Jingli Cai
- Department of Neuroscience, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Robyn Sussman
- Department of Cancer Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Guizhi Sun
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Sina K Kovermann
- Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Samanta A Mariani
- Department of Cancer Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Bruno Calabretta
- Department of Cancer Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Steven B McMahon
- Department of Cancer Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Hugh W Brock
- Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Lorraine Iacovitti
- Department of Neuroscience, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.
| | - Alexander Mazo
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.
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32
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Pluripotency of embryo-derived stem cells from rodents, lagomorphs, and primates: Slippery slope, terrace and cliff. Stem Cell Res 2017; 19:104-112. [DOI: 10.1016/j.scr.2017.01.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/01/2017] [Accepted: 01/13/2017] [Indexed: 12/14/2022] Open
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33
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Liu L, Michowski W, Inuzuka H, Shimizu K, Nihira NT, Chick JM, Li N, Geng Y, Meng AY, Ordureau A, Kołodziejczyk A, Ligon KL, Bronson RT, Polyak K, Harper JW, Gygi SP, Wei W, Sicinski P. G1 cyclins link proliferation, pluripotency and differentiation of embryonic stem cells. Nat Cell Biol 2017; 19:177-188. [PMID: 28192421 DOI: 10.1038/ncb3474] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 01/16/2017] [Indexed: 12/13/2022]
Abstract
Progression of mammalian cells through the G1 and S phases of the cell cycle is driven by the D-type and E-type cyclins. According to the current models, at least one of these cyclin families must be present to allow cell proliferation. Here, we show that several cell types can proliferate in the absence of all G1 cyclins. However, following ablation of G1 cyclins, embryonic stem (ES) cells attenuated their pluripotent characteristics, with the majority of cells acquiring the trophectodermal cell fate. We established that G1 cyclins, together with their associated cyclin-dependent kinases (CDKs), phosphorylate and stabilize the core pluripotency factors Nanog, Sox2 and Oct4. Treatment of murine ES cells, patient-derived glioblastoma tumour-initiating cells, or triple-negative breast cancer cells with a CDK inhibitor strongly decreased Sox2 and Oct4 levels. Our findings suggest that CDK inhibition might represent an attractive therapeutic strategy by targeting glioblastoma tumour-initiating cells, which depend on Sox2 to maintain their tumorigenic potential.
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Affiliation(s)
- Lijun Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Wojciech Michowski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Hiroyuki Inuzuka
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kouhei Shimizu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Naoe Taira Nihira
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Joel M Chick
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Na Li
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yan Geng
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Alice Y Meng
- Department of Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Aleksandra Kołodziejczyk
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Keith L Ligon
- Department of Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02215, USA
| | - Roderick T Bronson
- Department of Biomedical Sciences, Tufts University Veterinary School, North Grafton, Massachusetts 01536, USA
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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Fagnocchi L, Zippo A. Multiple Roles of MYC in Integrating Regulatory Networks of Pluripotent Stem Cells. Front Cell Dev Biol 2017; 5:7. [PMID: 28217689 PMCID: PMC5289991 DOI: 10.3389/fcell.2017.00007] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/20/2017] [Indexed: 12/20/2022] Open
Abstract
Pluripotent stem cells (PSCs) are defined by their self-renewal potential, which permits their unlimited propagation, and their pluripotency, being able to generate cell of the three embryonic lineages. These properties render PSCs a valuable tool for both basic and medical research. To induce and stabilize the pluripotent state, complex circuitries involving signaling pathways, transcription regulators and epigenetic mechanisms converge on a core transcriptional regulatory network of PSCs, thus determining their cell identity. Among the transcription factors, MYC represents a central hub, which modulates and integrates multiple mechanisms involved both in the maintenance of pluripotency and in cell reprogramming. Indeed, it instructs the PSC-specific cell cycle, metabolism and epigenetic landscape, contributes to limit exit from pluripotency and modulates signaling cascades affecting the PSC identity. Moreover, MYC extends its regulation on pluripotency by controlling PSC-specific non-coding RNAs. In this report, we review the MYC-controlled networks, which support the pluripotent state and discuss how their perturbation could affect cell identity. We further discuss recent finding demonstrating a central role of MYC in triggering epigenetic memory in PSCs, which depends on the establishment of a WNT-centered self-reinforcing circuit. Finally, we comment on the therapeutic implications of the role of MYC in affecting PSCs. Indeed, PSCs are used for both disease and cancer modeling and to derive cells for regenerative medicine. For these reasons, unraveling the MYC-mediated mechanism in those cells is fundamental to exploit their full potential and to identify therapeutic targets.
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Affiliation(s)
- Luca Fagnocchi
- Department of Epigenetics, Fondazione Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi" (INGM)Milan, Italy; Division of Pathology, Fondazione IRCCS Ca' Granda, Ospedale Maggiore PoliclinicoMilan, Italy
| | - Alessio Zippo
- Department of Epigenetics, Fondazione Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi" (INGM)Milan, Italy; Division of Pathology, Fondazione IRCCS Ca' Granda, Ospedale Maggiore PoliclinicoMilan, Italy
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35
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VanOudenhove JJ, Grandy RA, Ghule PN, Lian JB, Stein JL, Zaidi SK, Stein GS. Unique Regulatory Mechanisms for the Human Embryonic Stem Cell Cycle. J Cell Physiol 2017; 232:1254-1257. [PMID: 27532275 DOI: 10.1002/jcp.25567] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 08/16/2016] [Indexed: 12/14/2022]
Abstract
The cell cycle in pluripotent human embryonic stem cells is governed by unique mechanisms that support unrestricted proliferation and competency for endodermal, mesodermal, and ectodermal differentiation. The abbreviated G1 period with retention of uncompromised fidelity for genetic and epigenetic mechanisms operative in control of proliferation support competency for expansion of the pluripotent cell population that is fundamental for initial stages of development. Regulatory events during the G1 period of the pluripotent cell cycle are decisive for the transition from pluripotency to lineage commitment. Recent findings indicate that a G2 cell cycle pause is present in both endodermal and mesodermal lineage cells, and is obligatory for differentiation to endoderm. J. Cell. Physiol. 232: 1254-1257, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Jennifer J VanOudenhove
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, Burlington, Vermont
| | - Rodrigo A Grandy
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, Burlington, Vermont
| | - Prachi N Ghule
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, Burlington, Vermont
| | - Jane B Lian
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, Burlington, Vermont
| | - Janet L Stein
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, Burlington, Vermont
| | - Sayyed K Zaidi
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, Burlington, Vermont
| | - Gary S Stein
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, Burlington, Vermont
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36
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Herberg M, Glauche I, Zerjatke T, Winzi M, Buchholz F, Roeder I. Dissecting mechanisms of mouse embryonic stem cells heterogeneity through a model-based analysis of transcription factor dynamics. J R Soc Interface 2016; 13:rsif.2016.0167. [PMID: 27097654 DOI: 10.1098/rsif.2016.0167] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 03/29/2016] [Indexed: 01/06/2023] Open
Abstract
Pluripotent mouse embryonic stem cells (mESCs) show heterogeneous expression levels of transcription factors (TFs) involved in pluripotency regulation, among them Nanog and Rex1. The expression of both TFs can change dynamically between states of high and low activity, correlating with the cells' capacity for self-renewal. Stochastic fluctuations as well as sustained oscillations in gene expression are possible mechanisms to explain this behaviour, but the lack of suitable data hampered their clear distinction. Here, we present a systems biology approach in which novel experimental data on TF heterogeneity is complemented by an agent-based model of mESC self-renewal. Because the model accounts for intracellular interactions, cell divisions and heredity structures, it allows for evaluating the consistency of the proposed mechanisms with data on population growth and on TF dynamics after cell sorting. Our model-based analysis revealed that a bistable, noise-driven network model fulfils the minimal requirements to consistently explain Nanog and Rex1 expression dynamics in heterogeneous and sorted mESC populations. Moreover, we studied the impact of TF-related proliferation capacities on the frequency of state transitions and demonstrate that cellular genealogies can provide insights into the heredity structures of mESCs.
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Affiliation(s)
- Maria Herberg
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany Interdisciplinary Center for Bioinformatics, Faculty of Medicine, Universität Leipzig, Leipzig, Germany
| | - Ingmar Glauche
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Thomas Zerjatke
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Maria Winzi
- University Cancer Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Frank Buchholz
- University Cancer Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
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37
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Osteil P, Moulin A, Santamaria C, Joly T, Jouneau L, Aubry M, Tapponnier Y, Archilla C, Schmaltz-Panneau B, Lecardonnel J, Barasc H, Mouney-Bonnet N, Genthon C, Roulet A, Donnadieu C, Acloque H, Gocza E, Duranthon V, Afanassieff M, Savatier P. A Panel of Embryonic Stem Cell Lines Reveals the Variety and Dynamic of Pluripotent States in Rabbits. Stem Cell Reports 2016; 7:383-398. [PMID: 27594588 PMCID: PMC5032405 DOI: 10.1016/j.stemcr.2016.07.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 07/27/2016] [Accepted: 07/28/2016] [Indexed: 01/11/2023] Open
Abstract
Conventional rabbit embryonic stem cell (ESC) lines are derived from the inner cell mass (ICM) of pre-implantation embryos using methods and culture conditions that are established for primate ESCs. In this study, we explored the capacity of the rabbit ICM to give rise to ESC lines using conditions similar to those utilized to generate naive ESCs in mice. On single-cell dissociation and culture in fibroblast growth factor 2 (FGF2)-free, serum-supplemented medium, rabbit ICMs gave rise to ESC lines lacking the DNA-damage checkpoint in the G1 phase like mouse ESCs, and with a pluripotency gene expression profile closer to the rabbit ICM/epiblast profiles. These cell lines can be converted to FGF2-dependent ESCs after culture in conventional conditions. They can also colonize the rabbit pre-implantation embryo. These results indicate that rabbit epiblast cells can be coaxed toward different types of pluripotent stem cells and reveal the dynamics of pluripotent states in rabbit ESCs.
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Affiliation(s)
- Pierre Osteil
- Univ Lyon, Université Lyon 1, INSERM, Stem Cell and Brain Research Institute U1208, 69500 Bron, France; INRA, USC1361, 69500 Bron, France; Embryology Unit, Children's Medical Research Institute, CMRI, Westmead, NSW 2145, Australia
| | - Anaïs Moulin
- Univ Lyon, Université Lyon 1, INSERM, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Claire Santamaria
- Univ Lyon, Université Lyon 1, INSERM, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Thierry Joly
- ISARA-Lyon, 69007 Lyon, France; VetAgroSup, UPSP ICE, 69280 Marcy l'Etoile, France
| | - Luc Jouneau
- UMR BDR, INRA, ENVA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Maxime Aubry
- Univ Lyon, Université Lyon 1, INSERM, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Yann Tapponnier
- Univ Lyon, Université Lyon 1, INSERM, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Catherine Archilla
- UMR BDR, INRA, ENVA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | | | - Jérôme Lecardonnel
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Harmonie Barasc
- INRA, UMR 444, Génétique Cellulaire, 31076 Toulouse, France; ENVT, 31076 Toulouse, France
| | - Nathalie Mouney-Bonnet
- INRA, UMR 444, Génétique Cellulaire, 31076 Toulouse, France; ENVT, 31076 Toulouse, France
| | - Clémence Genthon
- INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, 31326 Castanet Tolosan, France
| | - Alain Roulet
- INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, 31326 Castanet Tolosan, France
| | - Cécile Donnadieu
- INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, 31326 Castanet Tolosan, France
| | - Hervé Acloque
- INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, 31326 Castanet Tolosan, France
| | - Elen Gocza
- NARIC, Agricultural Biotechnology Institute, 2100 Gödöllo, Hungary
| | | | - Marielle Afanassieff
- Univ Lyon, Université Lyon 1, INSERM, Stem Cell and Brain Research Institute U1208, 69500 Bron, France; INRA, USC1361, 69500 Bron, France.
| | - Pierre Savatier
- Univ Lyon, Université Lyon 1, INSERM, Stem Cell and Brain Research Institute U1208, 69500 Bron, France.
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38
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Histone modifications and p53 binding poise the p21 promoter for activation in human embryonic stem cells. Sci Rep 2016; 6:28112. [PMID: 27346849 PMCID: PMC4921813 DOI: 10.1038/srep28112] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 05/31/2016] [Indexed: 11/08/2022] Open
Abstract
The high proliferation rate of embryonic stem cells (ESCs) is thought to arise partly from very low expression of p21. However, how p21 is suppressed in ESCs has been unclear. We found that p53 binds to the p21 promoter in human ESCs (hESCs) as efficiently as in differentiated human mesenchymal stem cells, however it does not promote p21 transcription in hESCs. We observed an enrichment for both the repressive histone H3K27me3 and activating histone H3K4me3 chromatin marks at the p21 locus in hESCs, suggesting it is a suppressed, bivalent domain which overrides activation by p53. Reducing H3K27me3 methylation in hESCs rescued p21 expression, and ectopic expression of p21 in hESCs triggered their differentiation. Further, we uncovered a subset of bivalent promoters bound by p53 in hESCs that are similarly induced upon differentiation in a p53-dependent manner, whereas p53 promotes the transcription of other target genes which do not show an enrichment of H3K27me3 in ESCs. Our studies reveal a unique epigenetic strategy used by ESCs to poise undesired p53 target genes, thus balancing the maintenance of pluripotency in the undifferentiated state with a robust response to differentiation signals, while utilizing p53 activity to maintain genomic stability and homeostasis in ESCs.
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39
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Kramer N, Rosner M, Kovacic B, Hengstschläger M. Full biological characterization of human pluripotent stem cells will open the door to translational research. Arch Toxicol 2016; 90:2173-2186. [PMID: 27325309 DOI: 10.1007/s00204-016-1763-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 06/13/2016] [Indexed: 12/13/2022]
Abstract
Since the discovery of human embryonic stem cells (hESC) and human-induced pluripotent stem cells (hiPSC), great hopes were held for their therapeutic application including disease modeling, drug discovery screenings, toxicological screenings and regenerative therapy. hESC and hiPSC have the advantage of indefinite self-renewal, thereby generating an inexhaustible pool of cells with, e.g., specific genotype for developing putative treatments; they can differentiate into derivatives of all three germ layers enabling autologous transplantation, and via donor-selection they can express various genotypes of interest for better disease modeling. Furthermore, drug screenings and toxicological screenings in hESC and hiPSC are more pertinent to identify drugs or chemical compounds that are harmful for human, than a mouse model could predict. Despite continuing research in the wide field of therapeutic applications, further understanding of the underlying basic mechanisms of stem cell function is necessary. Here, we summarize current knowledge concerning pluripotency, self-renewal, apoptosis, motility, epithelial-to-mesenchymal transition and differentiation of pluripotent stem cells.
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Affiliation(s)
- Nina Kramer
- Institute of Medical Genetics, Medical University of Vienna, Währingerstrasse 10, 1090, Vienna, Austria
| | - Margit Rosner
- Institute of Medical Genetics, Medical University of Vienna, Währingerstrasse 10, 1090, Vienna, Austria
| | - Boris Kovacic
- Institute of Medical Genetics, Medical University of Vienna, Währingerstrasse 10, 1090, Vienna, Austria
| | - Markus Hengstschläger
- Institute of Medical Genetics, Medical University of Vienna, Währingerstrasse 10, 1090, Vienna, Austria.
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40
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Singh AM, Trost R, Boward B, Dalton S. Utilizing FUCCI reporters to understand pluripotent stem cell biology. Methods 2016; 101:4-10. [PMID: 26404921 PMCID: PMC4801677 DOI: 10.1016/j.ymeth.2015.09.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 09/15/2015] [Accepted: 09/20/2015] [Indexed: 11/27/2022] Open
Abstract
The fluorescence ubiquitination cell cycle indicator (FUCCI) system provides a powerful method to evaluate cell cycle mechanisms associated with stem cell self-renewal and cell fate specification. By integrating the FUCCI system into human pluripotent stem cells (hPSCs) it is possible to isolate homogeneous fractions of viable cells representative of all cell cycle phases. This method avoids problems associated with traditional tools used for cell cycle analysis such as synchronizing drugs, elutriation and temperature sensitive mutants. Importantly, FUCCI reporters allow cell cycle events in dynamic systems, such as differentiation, to be evaluated. Initial reports on the FUCCI system focused on its strengths in reporting spatio-temporal aspects of cell cycle events in living cells and developmental models. In this report, we describe approaches that broaden the application of FUCCI reporters in PSCs through incorporation of FACS. This approach allows molecular analysis of the cell cycle in stem cell systems that were not previously possible.
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Affiliation(s)
- Amar M Singh
- Department of Biochemistry and Molecular Biology, Paul D. Coverdell Center for Biomedical and Health Sciences, The University of Georgia, 500 D.W. Brooks Drive, Athens, GA 30602, USA
| | - Robert Trost
- Department of Biochemistry and Molecular Biology, Paul D. Coverdell Center for Biomedical and Health Sciences, The University of Georgia, 500 D.W. Brooks Drive, Athens, GA 30602, USA
| | - Benjamin Boward
- Department of Biochemistry and Molecular Biology, Paul D. Coverdell Center for Biomedical and Health Sciences, The University of Georgia, 500 D.W. Brooks Drive, Athens, GA 30602, USA
| | - Stephen Dalton
- Department of Biochemistry and Molecular Biology, Paul D. Coverdell Center for Biomedical and Health Sciences, The University of Georgia, 500 D.W. Brooks Drive, Athens, GA 30602, USA.
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41
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Van Oudenhove JJ, Grandy RA, Ghule PN, Del Rio R, Lian JB, Stein JL, Zaidi SK, Stein GS. Lineage-Specific Early Differentiation of Human Embryonic Stem Cells Requires a G2 Cell Cycle Pause. Stem Cells 2016; 34:1765-75. [PMID: 26946228 DOI: 10.1002/stem.2352] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/07/2016] [Indexed: 12/14/2022]
Abstract
Human embryonic stem cells (hESCs) have an abbreviated G1 phase of the cell cycle that allows rapid proliferation and maintenance of pluripotency. Lengthening of G1 corresponds to loss of pluripotency during differentiation. However, precise mechanisms that link alterations in the cell cycle and early differentiation remain to be defined. We investigated initial stages of mesendodermal lineage commitment in hESCs, and observed a cell cycle pause. Transcriptome profiling identified several genes with known roles in regulation of the G2/M transition that were differentially expressed early during lineage commitment. WEE1 kinase, which blocks entry into mitosis by phosphorylating CDK1 at Y15, was the most highly expressed of these genes. Inhibition of CDK1 phosphorylation by a specific inhibitor of WEE1 restored cell cycle progression by preventing the G2 pause. Directed differentiation of hESCs revealed that cells paused during commitment to the endo- and mesodermal, but not ectodermal, lineages. Functionally, WEE1 inhibition during meso- and endodermal differentiation selectively decreased expression of definitive endodermal markers SOX17 and FOXA2. Our findings identify a novel G2 cell cycle pause that is required for endodermal differentiation and provide important new mechanistic insights into early events of lineage commitment. Stem Cells 2016;34:1765-1775.
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Affiliation(s)
| | - Rodrigo A Grandy
- Department of Biochemistry and University of Vermont Cancer Center, Burlington, VT, USA
| | - Prachi N Ghule
- Department of Biochemistry and University of Vermont Cancer Center, Burlington, VT, USA
| | - Roxana Del Rio
- Department of Surgery and Flow Cytometry & Cell Sorting Facility, University of Vermont College of Medicine, Burlington, VT, USA
| | - Jane B Lian
- Department of Biochemistry and University of Vermont Cancer Center, Burlington, VT, USA
| | - Janet L Stein
- Department of Biochemistry and University of Vermont Cancer Center, Burlington, VT, USA
| | - Sayyed K Zaidi
- Department of Biochemistry and University of Vermont Cancer Center, Burlington, VT, USA
| | - Gary S Stein
- Department of Biochemistry and University of Vermont Cancer Center, Burlington, VT, USA
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42
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Boward B, Wu T, Dalton S. Concise Review: Control of Cell Fate Through Cell Cycle and Pluripotency Networks. Stem Cells 2016; 34:1427-36. [PMID: 26889666 DOI: 10.1002/stem.2345] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 01/20/2016] [Accepted: 01/29/2016] [Indexed: 01/04/2023]
Abstract
Pluripotent stem cells (PSCs) proliferate rapidly with a characteristic cell cycle structure consisting of short G1- and G2-gap phases. This applies broadly to PSCs of peri-implantation stage embryos, cultures of embryonic stem cells, induced pluripotent stem cells, and embryonal carcinoma cells. During the early stages of PSC differentiation however, cell division times increase as a consequence of cell cycle remodeling. Most notably, this is indicated by elongation of the G1-phase. Observations linking changes in the cell cycle with exit from pluripotency have raised questions about the role of cell cycle control in maintenance of the pluripotent state. Until recently however, this has been a difficult question to address because of limitations associated with experimental tools. Recent studies now show that pluripotency and cell cycle regulatory networks are intertwined and that cell cycle control mechanisms are an integral, mechanistic part of the PSC state. Studies in embryonal carcinoma, some 30 years ago, first suggested that pluripotent cells initiate differentiation when in the G1-phase. More recently, a molecular "priming" mechanism has been proposed to explain these observations in human embryonic stem cells. Complexity in this area has been increased by the realization that pluripotent cells exist in multiple developmental states and that in addition to each having their own characteristic gene expression and epigenetic signatures, they potentially have alternate modes of cell cycle regulation. This review will summarize current knowledge in these areas and will highlight important aspects of interconnections between the cell cycle, self-renewal, pluripotency, and cell fate decisions. Stem Cells 2016;34:1427-1436.
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Affiliation(s)
- Ben Boward
- Department of Biochemistry and Molecular Biology, Center for Molecular Medicine, Paul D. Coverdell Center for Biomedical and Health Sciences, The University of Georgia, Athens, Georgia, USA
| | - Tianming Wu
- Department of Biochemistry and Molecular Biology, Center for Molecular Medicine, Paul D. Coverdell Center for Biomedical and Health Sciences, The University of Georgia, Athens, Georgia, USA
| | - Stephen Dalton
- Department of Biochemistry and Molecular Biology, Center for Molecular Medicine, Paul D. Coverdell Center for Biomedical and Health Sciences, The University of Georgia, Athens, Georgia, USA
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43
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Lanza DG, Dawson EP, Rao P, Heaney JD. Misexpression of cyclin D1 in embryonic germ cells promotes testicular teratoma initiation. Cell Cycle 2016; 15:919-30. [PMID: 26901436 DOI: 10.1080/15384101.2016.1149272] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Testicular teratomas result from anomalies in embryonic germ cell development. In the 129 family of inbred mouse strains, teratomas arise during the same developmental period that male germ cells normally enter G1/G0 mitotic arrest and female germ cells initiate meiosis (the mitotic:meiotic switch). Dysregulation of this switch associates with teratoma susceptibility and involves three germ cell developmental abnormalities seemingly critical for tumor initiation: delayed G1/G0 mitotic arrest, retention of pluripotency, and misexpression of genes normally restricted to embryonic female and adult male germ cells. One misexpressed gene, cyclin D1 (Ccnd1), is a known regulator of cell cycle progression and an oncogene in many tissues. Here, we investigated whether Ccnd1 misexpression in embryonic germ cells is a determinant of teratoma susceptibility in mice. We found that CCND1 localizes to teratoma-susceptible germ cells that fail to enter G1/G0 arrest during the mitotic:meiotic switch and is the only D-type cyclin misexpressed during this critical developmental time frame. We discovered that Ccnd1 deficiency in teratoma-susceptible mice significantly reduced teratoma incidence and suppressed the germ cell proliferation and pluripotency abnormalities associated with tumor initiation. Importantly, Ccnd1 expression was dispensable for somatic cell development and male germ cell specification and maturation in tumor-susceptible mice, implying that the mechanisms by which Ccnd1 deficiency reduced teratoma incidence were germ cell autonomous and specific to tumorigenesis. We conclude that misexpression of Ccnd1 in male germ cells is a key component of a larger pro-proliferative program that disrupts the mitotic:meiotic switch and predisposes 129 inbred mice to testicular teratocarcinogenesis.
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Affiliation(s)
- Denise G Lanza
- a Department of Molecular and Human Genetics , Baylor College of Medicine , Houston , TX , USA
| | - Emily P Dawson
- a Department of Molecular and Human Genetics , Baylor College of Medicine , Houston , TX , USA
| | - Priya Rao
- b Department of Pathology , MD Anderson Cancer Center, The University of Texas , Houston , TX , USA
| | - Jason D Heaney
- a Department of Molecular and Human Genetics , Baylor College of Medicine , Houston , TX , USA.,c Dan L Duncan Cancer Center, Baylor College of Medicine , Houston , TX , USA.,d Center For Reproductive Medicine, Baylor College of Medicine , Houston , TX , USA
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Matsu-ura T, Sasaki H, Okada M, Mikoshiba K, Ashraf M. Attenuation of teratoma formation by p27 overexpression in induced pluripotent stem cells. Stem Cell Res Ther 2016; 7:30. [PMID: 26880084 PMCID: PMC4754927 DOI: 10.1186/s13287-016-0286-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 11/26/2015] [Accepted: 01/20/2016] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Pluripotent stem cells, such as embryonic stem cells or induced pluripotent stem cells, have a great potential for regenerative medicine. Induced pluripotent stem cells, in particular, are suitable for replacement of tissue by autologous transplantation. However, tumorigenicity is a major risk in clinical application of both embryonic stem cells and induced pluripotent stem cells. This study explores the possibility of manipulating the cell cycle for inhibition of tumorigenicity. METHODS We genetically modified mouse induced pluripotent stem cells (miPSCs) to overexpress p27 tumor suppressor and examined their proliferation rate, gene expression, cardiac differentiation, tumorigenicity, and therapeutic potential in a mouse model of coronary artery ligation. RESULTS Overexpression of p27 inhibited cell division of miPSCs, and that inhibition was dependent on the expression level of p27. p27 overexpressing miPSCs had pluripotency characteristics but lost stemness earlier than normal miPSCs during embryoid body and teratoma formation. These cellular characteristics led to none or smaller teratoma when the cells were injected into nude mice. Transplantation of both miPSCs and p27 overexpressing miPSCs into the infarcted mouse heart reduced the infarction size and improved left ventricular function. CONCLUSIONS The overexpression of p27 attenuated tumorigenicity by reducing proliferation and earlier loss of stemness of miPSCs. The overexpression of p27 did not affect pluripotency and differentiation characteristics of miPSC. Therefore, regulation of the proliferation rate of miPSCs offers great therapeutic potential for repair of the injured myocardium.
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Affiliation(s)
- Toru Matsu-ura
- Department of Pathology and Laboratory Medicine, University of Cincinnati, Cincinnati, OH, 45267-0529, USA.
| | - Hiroshi Sasaki
- Department of Pathology and Laboratory Medicine, University of Cincinnati, Cincinnati, OH, 45267-0529, USA.
| | - Motoi Okada
- Department of Pathology and Laboratory Medicine, University of Cincinnati, Cincinnati, OH, 45267-0529, USA.
| | - Katsuhiko Mikoshiba
- Laboratory for Developmental Neurobiology, RIKEN Brain Science Institute, Saitama, 351-0198, Japan.
| | - Muhammad Ashraf
- Department of Pathology and Laboratory Medicine, University of Cincinnati, Cincinnati, OH, 45267-0529, USA. .,Department of Pharmacology, University of Illinois at Chicago College of Medicine, 835 South Wolcott Ave, Chicago, IL, 60612, USA.
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Julian LM, Carpenedo RL, Rothberg JLM, Stanford WL. Formula G1: Cell cycle in the driver's seat of stem cell fate determination. Bioessays 2016; 38:325-32. [DOI: 10.1002/bies.201500187] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Lisa M. Julian
- Sprott Centre for Stem Cell Research; Regenerative Medicine Program; Ottawa Hospital Research Institute; Ottawa ON Canada
- Faculty of Graduate and Postdoctoral Studies; Ottawa; ON Canada
| | - Richard L. Carpenedo
- Sprott Centre for Stem Cell Research; Regenerative Medicine Program; Ottawa Hospital Research Institute; Ottawa ON Canada
- Faculty of Graduate and Postdoctoral Studies; Ottawa; ON Canada
| | - Janet L. Manias Rothberg
- Sprott Centre for Stem Cell Research; Regenerative Medicine Program; Ottawa Hospital Research Institute; Ottawa ON Canada
- Faculty of Graduate and Postdoctoral Studies; Ottawa; ON Canada
- Department of Cellular and Molecular Medicine; University of Ottawa; Ottawa ON Canada
| | - William L. Stanford
- Sprott Centre for Stem Cell Research; Regenerative Medicine Program; Ottawa Hospital Research Institute; Ottawa ON Canada
- Faculty of Graduate and Postdoctoral Studies; Ottawa; ON Canada
- Department of Cellular and Molecular Medicine; University of Ottawa; Ottawa ON Canada
- Department of Biochemistry; Microbiology and Immunology; University of Ottawa; Ottawa ON Canada
- Ottawa Institute of Systems Biology; Ottawa; Ontario Canada
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El-Badawy A, El-Badri N. The cell cycle as a brake for β-cell regeneration from embryonic stem cells. Stem Cell Res Ther 2016; 7:9. [PMID: 26759123 PMCID: PMC4711007 DOI: 10.1186/s13287-015-0274-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The generation of insulin-producing β cells from stem cells in vitro provides a promising source of cells for cell transplantation therapy in diabetes. However, insulin-producing cells generated from human stem cells show deficiency in many functional characteristics compared with pancreatic β cells. Recent reports have shown molecular ties between the cell cycle and the differentiation mechanism of embryonic stem (ES) cells, assuming that cell fate decisions are controlled by the cell cycle machinery. Both β cells and ES cells possess unique cell cycle machinery yet with significant contrasts. In this review, we compare the cell cycle control mechanisms in both ES cells and β cells, and highlight the fundamental differences between pluripotent cells of embryonic origin and differentiated β cells. Through critical analysis of the differences of the cell cycle between these two cell types, we propose that the cell cycle of ES cells may act as a brake for β-cell regeneration. Based on these differences, we discuss the potential of modulating the cell cycle of ES cells for the large-scale generation of functionally mature β cells in vitro. Further understanding of the factors that modulate the ES cell cycle will lead to new approaches to enhance the production of functional mature insulin-producing cells, and yield a reliable system to generate bona fide β cells in vitro.
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Affiliation(s)
- Ahmed El-Badawy
- Center of Excellence for Stem Cells and Regenerative Medicine (CESC), Zewail City of Science and Technology, Sheikh Zayed District, 12588, 6th of October City, Giza, Egypt
| | - Nagwa El-Badri
- Center of Excellence for Stem Cells and Regenerative Medicine (CESC), Zewail City of Science and Technology, Sheikh Zayed District, 12588, 6th of October City, Giza, Egypt.
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Shimba K, Iida S, Kotani K, Jimbo Y. Cell-cycle-dependent Ca2+ transients in human induced pluripotent stem cells revealed by a simultaneous imaging of cell nuclei and intracellular Ca2+ level. Integr Biol (Camb) 2016; 8:985-990. [DOI: 10.1039/c6ib00074f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Simultaneous imaging of cell nuclei and intracellular Ca2+ level revealed that human iPS cells exhibited cell cycle-dependent Ca2+ transients.
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Affiliation(s)
- Kenta Shimba
- School of Engineering
- The University of Tokyo
- Tokyo
- Japan
- School of Engineering
| | - Shoko Iida
- School of Engineering
- The University of Tokyo
- Tokyo
- Japan
| | - Kiyoshi Kotani
- Research Center for Advanced Science and Technology
- The University of Tokyo
- Tokyo
- Japan
- PRESTO
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48
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Ruijtenberg S, van den Heuvel S. Coordinating cell proliferation and differentiation: Antagonism between cell cycle regulators and cell type-specific gene expression. Cell Cycle 2016; 15:196-212. [PMID: 26825227 PMCID: PMC4825819 DOI: 10.1080/15384101.2015.1120925] [Citation(s) in RCA: 360] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/04/2015] [Accepted: 11/12/2015] [Indexed: 11/25/2022] Open
Abstract
Cell proliferation and differentiation show a remarkable inverse relationship. Precursor cells continue division before acquiring a fully differentiated state, while terminal differentiation usually coincides with proliferation arrest and permanent exit from the division cycle. Mechanistic insight in the temporal coordination between cell cycle exit and differentiation has come from studies of cells in culture and genetic animal models. As initially described for skeletal muscle differentiation, temporal coordination involves mutual antagonism between cyclin-dependent kinases that promote cell cycle entry and transcription factors that induce tissue-specific gene expression. Recent insights highlight the contribution of chromatin-regulating complexes that act in conjunction with the transcription factors and determine their activity. In particular SWI/SNF chromatin remodelers contribute to dual regulation of cell cycle and tissue-specific gene expression during terminal differentiation. We review the concerted regulation of the cell cycle and cell type-specific transcription, and discuss common mutations in human cancer that emphasize the clinical importance of proliferation versus differentiation control.
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Affiliation(s)
- Suzan Ruijtenberg
- Developmental Biology, Department of Biology, Faculty of Sciences, Utrecht University, Utrecht, The Netherlands
| | - Sander van den Heuvel
- Developmental Biology, Department of Biology, Faculty of Sciences, Utrecht University, Utrecht, The Netherlands
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Gorman BR, Lu J, Baccei A, Lowry NC, Purvis JE, Mangoubi RS, Lerou PH. Multi-scale imaging and informatics pipeline for in situ pluripotent stem cell analysis. PLoS One 2014; 9:e116037. [PMID: 25551762 PMCID: PMC4281228 DOI: 10.1371/journal.pone.0116037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 12/01/2014] [Indexed: 01/01/2023] Open
Abstract
Human pluripotent stem (hPS) cells are a potential source of cells for medical therapy and an ideal system to study fate decisions in early development. However, hPS cells cultured in vitro exhibit a high degree of heterogeneity, presenting an obstacle to clinical translation. hPS cells grow in spatially patterned colony structures, necessitating quantitative single-cell image analysis. We offer a tool for analyzing the spatial population context of hPS cells that integrates automated fluorescent microscopy with an analysis pipeline. It enables high-throughput detection of colonies at low resolution, with single-cellular and sub-cellular analysis at high resolutions, generating seamless in situ maps of single-cellular data organized by colony. We demonstrate the tool's utility by analyzing inter- and intra-colony heterogeneity of hPS cell cycle regulation and pluripotency marker expression. We measured the heterogeneity within individual colonies by analyzing cell cycle as a function of distance. Cells loosely associated with the outside of the colony are more likely to be in G1, reflecting a less pluripotent state, while cells within the first pluripotent layer are more likely to be in G2, possibly reflecting a G2/M block. Our multi-scale analysis tool groups colony regions into density classes, and cells belonging to those classes have distinct distributions of pluripotency markers and respond differently to DNA damage induction. Lastly, we demonstrate that our pipeline can robustly handle high-content, high-resolution single molecular mRNA FISH data by using novel image processing techniques. Overall, the imaging informatics pipeline presented offers a novel approach to the analysis of hPS cells that includes not only single cell features but also colony wide, and more generally, multi-scale spatial configuration.
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Affiliation(s)
- Bryan R. Gorman
- Department Of Pediatric Newborn Medicine and Department of Medicine, Division of Genetics, Brigham and Women's Hospital; Harvard Medical School; Harvard Stem Cell Institute, Boston, Massachusetts, United States of America
- Harvard-MIT Division Of Health Sciences and Technology, Massachusetts Institute Of Technology, Cambridge, Massachusetts, United States of America
- Charles Stark Draper Laboratory, Cambridge, Massachusetts, United States of America
| | - Junjie Lu
- Department Of Pediatric Newborn Medicine and Department of Medicine, Division of Genetics, Brigham and Women's Hospital; Harvard Medical School; Harvard Stem Cell Institute, Boston, Massachusetts, United States of America
| | - Anna Baccei
- Department Of Pediatric Newborn Medicine and Department of Medicine, Division of Genetics, Brigham and Women's Hospital; Harvard Medical School; Harvard Stem Cell Institute, Boston, Massachusetts, United States of America
| | - Nathan C. Lowry
- Charles Stark Draper Laboratory, Cambridge, Massachusetts, United States of America
| | - Jeremy E. Purvis
- Department Of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Rami S. Mangoubi
- Charles Stark Draper Laboratory, Cambridge, Massachusetts, United States of America
| | - Paul H. Lerou
- Department Of Pediatric Newborn Medicine and Department of Medicine, Division of Genetics, Brigham and Women's Hospital; Harvard Medical School; Harvard Stem Cell Institute, Boston, Massachusetts, United States of America
- * E-mail:
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50
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Wu J, Fan Y, Tzanakakis ES. Increased culture density is linked to decelerated proliferation, prolonged G1 phase, and enhanced propensity for differentiation of self-renewing human pluripotent stem cells. Stem Cells Dev 2014; 24:892-903. [PMID: 25405279 DOI: 10.1089/scd.2014.0384] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) display a very short G1 phase and rapid proliferation kinetics. Regulation of the cell cycle, which is linked to pluripotency and differentiation, is dependent on the stem cell environment, particularly on culture density. This link has been so far empirical and central to disparities in the growth rates and fractions of self-renewing hPSCs residing in different cycle phases. In this study, hPSC cycle progression in conjunction with proliferation and differentiation were comprehensively investigated for different culture densities. Cell proliferation decelerated significantly at densities beyond 50×10(4) cells/cm(2). Correspondingly, the G1 fraction increased from 25% up to 60% at densities greater than 40×10(4) cells/cm(2) while still hPSC pluripotency marker expression was maintained. In parallel, expression of the cycle inhibitor CDKN1A (p21) was increased, while that of p27 and p53 did not change significantly. After 4 days of culture in an unconditioned medium, greater heterogeneity was noted in the differentiation outcomes and was limited by reducing the density variation. A quantitative model was constructed for self-renewing and differentiating hPSC ensembles to gain a better understanding of the link between culture density, cycle progression, and stem cell state. Results for multiple hPSC lines and medium types corroborated experimental findings. Media commonly used for maintenance of self-renewing hPSCs exhibited the slowest kinetics of induction of differentiation (kdiff), while BMP4 supplementation led to 14-fold higher kdiff values. Spontaneous differentiation in a growth factor-free medium exhibited the largest variation in outcomes at different densities. In conjunction with the quantitative framework, our findings will facilitate rationalizing the selection of cultivation conditions for the generation of stem cell therapeutics.
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Affiliation(s)
- Jincheng Wu
- Department of Chemical and Biological Engineering, Tufts University , Medford, Massachusetts
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