1
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Ghasemi N, Azizi H. Exploring Myc puzzle: Insights into cancer, stem cell biology, and PPI networks. Gene 2024; 916:148447. [PMID: 38583818 DOI: 10.1016/j.gene.2024.148447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 03/13/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
Abstract
"The grand orchestrator," "Universal Amplifier," "double-edged sword," and "Undruggable" are just some of the Myc oncogene so-called names. It has been around 40 years since the discovery of the Myc, and it remains in the mainstream of cancer treatment drugs. Myc is part of basic helix-loop-helix leucine zipper (bHLH-LZ) superfamily proteins, and its dysregulation can be seen in many malignant human tumors. It dysregulates critical pathways in cells that are connected to each other, such as proliferation, growth, cell cycle, and cell adhesion, impacts miRNAs action, intercellular metabolism, DNA replication, differentiation, microenvironment regulation, angiogenesis, and metastasis. Myc, surprisingly, is used in stem cell research too. Its family includes three members, MYC, MYCN, and MYCL, and each dysfunction was observed in different cancer types. This review aims to introduce Myc and its function in the body. Besides, Myc deregulatory mechanisms in cancer cells, their intricate aspects will be discussed. We will look at promising drugs and Myc-based therapies. Finally, Myc and its role in stemness, Myc pathways based on PPI network analysis, and future insights will be explained.
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Affiliation(s)
- Nima Ghasemi
- Faculty of Biotechnology, Amol University of Special Modern Technologies, Amol, Iran
| | - Hossein Azizi
- Faculty of Biotechnology, Amol University of Special Modern Technologies, Amol, Iran.
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2
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Mark KG, Kolla S, Aguirre JD, Garshott DM, Schmitt S, Haakonsen DL, Xu C, Kater L, Kempf G, Martínez-González B, Akopian D, See SK, Thomä NH, Rapé M. Orphan quality control shapes network dynamics and gene expression. Cell 2023; 186:3460-3475.e23. [PMID: 37478862 DOI: 10.1016/j.cell.2023.06.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 04/13/2023] [Accepted: 06/21/2023] [Indexed: 07/23/2023]
Abstract
All eukaryotes require intricate protein networks to translate developmental signals into accurate cell fate decisions. Mutations that disturb interactions between network components often result in disease, but how the composition and dynamics of complex networks are established remains poorly understood. Here, we identify the E3 ligase UBR5 as a signaling hub that helps degrade unpaired subunits of multiple transcriptional regulators that act within a network centered on the c-Myc oncoprotein. Biochemical and structural analyses show that UBR5 binds motifs that only become available upon complex dissociation. By rapidly turning over unpaired transcription factor subunits, UBR5 establishes dynamic interactions between transcriptional regulators that allow cells to effectively execute gene expression while remaining receptive to environmental signals. We conclude that orphan quality control plays an essential role in establishing dynamic protein networks, which may explain the conserved need for protein degradation during transcription and offers opportunities to modulate gene expression in disease.
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Affiliation(s)
- Kevin G Mark
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - SriDurgaDevi Kolla
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Jacob D Aguirre
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Danielle M Garshott
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Stefan Schmitt
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Diane L Haakonsen
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA
| | - Christina Xu
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Lukas Kater
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Georg Kempf
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Brenda Martínez-González
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - David Akopian
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Stephanie K See
- Center for Emerging and Neglected Diseases, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
| | - Michael Rapé
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California at Berkeley, Berkeley, CA 94720, USA.
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3
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Wang J, Zhang C, Huang Y, Ruan Y, Hu Y, Wang J, Wang F, Yu M, Xu Y, Liu L, Cheng Y, Yang R, Dong Y, Wang J, Yang Y, Xiong J, Tian Y, Gao Q, Zhang J, Jian R. Parallel Genome-Wide CRISPR Screens to Identify State-Dependent Self-Renewal Regulators of Mouse Embryonic Stem Cells. Stem Cells Dev 2023; 32:450-464. [PMID: 37166379 DOI: 10.1089/scd.2023.0053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
The pluripotency of embryonic stem cells (ESCs) is more accurately viewed as a continuous developmental process rather than a fixed state. However, the factors that play general or state-specific roles in regulating self-renewal in different pluripotency states remain poorly defined. In this study, parallel genome-wide CRISPR/Cas9 knockout (KO) screens were applied in ESCs cultured in the serum plus LIF (SL) and in the 2i plus LIF (2iL) conditions. The candidate genes were classified into seven groups based on their positive or negative effects on self-renewal, and whether this effect was general or state-specific for ESCs under SL and 2iL culture conditions. We characterized the expression and function of genes in these seven groups. The loss of function of novel pluripotent candidate genes Usp28, Zfp598, and Zfp296 was further evaluated in mouse ESCs. Consistent with our screen, the knockout of Usp28 promotes the proliferation of SL-ESCs and 2iL-ESCs, whereas Zfp598 is indispensable for the self-renewal of ESCs under both culture conditions. The cell phenotypes of Zfp296 KO ESCs under SL and 2iL culture conditions were different. Our work provided a valuable resource for dissecting the molecular regulation of ESC self-renewal in different pluripotency states.
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Affiliation(s)
- Jiangjun Wang
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
- Department of Cell Biology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Chen Zhang
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Yi Huang
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Yan Ruan
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Yan Hu
- Department of Military Basic Training and Army Management, Army Health Service Training Base, Army Medical University, Chongqing, China
| | - Jiaqi Wang
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
- Department of Pathophysiology, College of High-Altitude Military Medicine, Army Medical University, Chongqing, China
| | - Fengsheng Wang
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
- State Key Laboratory of NBC Protection for Civilian, Beijing, China
| | - Meng Yu
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
- Department of Joint Surgery, Southwest Hospital, the First Hospital Affiliated to Army Medical University, Chongqing, China
| | - Yixiao Xu
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Lianlian Liu
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Yuda Cheng
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Ran Yang
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
- Department of Pathophysiology, College of High-Altitude Military Medicine, Army Medical University, Chongqing, China
| | - Yutong Dong
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
- Department of Military Basic Training and Army Management, Army Health Service Training Base, Army Medical University, Chongqing, China
| | - Jiali Wang
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Yi Yang
- Experimental Center of Basic Medicine, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Jiaxiang Xiong
- Experimental Center of Basic Medicine, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Yanping Tian
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Qiangguo Gao
- Department of Cell Biology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Junlei Zhang
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Rui Jian
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
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4
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Fan W, Li X. The SIRT1-c-Myc axis in regulation of stem cells. Front Cell Dev Biol 2023; 11:1236968. [PMID: 37554307 PMCID: PMC10405831 DOI: 10.3389/fcell.2023.1236968] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 07/10/2023] [Indexed: 08/10/2023] Open
Abstract
SIRT1 is the most conserved mammalian NAD+-dependent protein deacetylase. Through deacetylation of transcriptional factors and co-factors, this protein modification enzyme is critically involved in metabolic and epigenetic regulation of stem cells, which is functionally important in maintaining their pluripotency and regulating their differentiation. C-Myc, a key member of Myc proton-oncogene family, is a pivotal factor for transcriptional regulation of genes that control acquisition and maintenance of stemness. Previous cancer research has revealed an intriguing positive feedback loop between SIRT1 and c-Myc that is crucial in tumorigenesis. Recent literature has uncovered important functions of this axis in regulation of maintenance and differentiation of stem cells, including pluripotent stem cells and cancer stem cells. This review highlights recent advances of the SIRT1-c-Myc axis in stem cells.
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Affiliation(s)
- Wei Fan
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, United States
| | - Xiaoling Li
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, United States
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5
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Ruan Y, Wang J, Yu M, Wang F, Wang J, Xu Y, Liu L, Cheng Y, Yang R, Zhang C, Yang Y, Wang J, Wu W, Huang Y, Tian Y, Chen G, Zhang J, Jian R. A multi-omics integrative analysis based on CRISPR screens re-defines the pluripotency regulatory network in ESCs. Commun Biol 2023; 6:410. [PMID: 37059858 PMCID: PMC10104827 DOI: 10.1038/s42003-023-04700-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/13/2023] [Indexed: 04/16/2023] Open
Abstract
A comprehensive and precise definition of the pluripotency gene regulatory network (PGRN) is crucial for clarifying the regulatory mechanisms in embryonic stem cells (ESCs). Here, after a CRISPR/Cas9-based functional genomics screen and integrative analysis with other functional genomes, transcriptomes, proteomes and epigenome data, an expanded pluripotency-associated gene set is obtained, and a new PGRN with nine sub-classes is constructed. By integrating the DNA binding, epigenetic modification, chromatin conformation, and RNA expression profiles, the PGRN is resolved to six functionally independent transcriptional modules (CORE, MYC, PAF, PRC, PCGF and TBX). Spatiotemporal transcriptomics reveal activated CORE/MYC/PAF module activity and repressed PRC/PCGF/TBX module activity in both mouse ESCs (mESCs) and pluripotent cells of early embryos. Moreover, this module activity pattern is found to be shared by human ESCs (hESCs) and cancers. Thus, our results provide novel insights into elucidating the molecular basis of ESC pluripotency.
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Affiliation(s)
- Yan Ruan
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Jiaqi Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Pathophysiology, College of High Altitude Military Medicine, Army Medical University, Chongqing, 400038, China
| | - Meng Yu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Joint Surgery, The First Affiliated Hospital, Army Medical University, Chongqing, 400038, China
| | - Fengsheng Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
| | - Jiangjun Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Cell Biology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Yixiao Xu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Lianlian Liu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Yuda Cheng
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Ran Yang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Pathophysiology, College of High Altitude Military Medicine, Army Medical University, Chongqing, 400038, China
| | - Chen Zhang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Yi Yang
- Experimental Center of Basic Medicine, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - JiaLi Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Wei Wu
- Thoracic Surgery Department, Southwest Hospital, The First Hospital Affiliated to Army Medical University, Chongqing, 400038, China
| | - Yi Huang
- Biomedical Analysis Center, Army Medical University, Chongqing, 400038, China
| | - Yanping Tian
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Guangxing Chen
- Department of Joint Surgery, The First Affiliated Hospital, Army Medical University, Chongqing, 400038, China.
| | - Junlei Zhang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China.
| | - Rui Jian
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China.
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6
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Spiller C, Bowles J. Instructing Mouse Germ Cells to Adopt a Female Fate. Sex Dev 2022:1-13. [PMID: 35320803 DOI: 10.1159/000523763] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 02/20/2022] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Germ cells are critical for the survival of our species. They are the only cells that undergo meiosis - the reductive form of cell division that is necessary for genetic reassortment of chromosomes and production of the haploid gametes, the sperm and eggs. Remarkably, the initial female/male fate decision in fetal germ cells does not depend on whether they are chromosomally XX or XY; rather, initial sexual fate is imposed by influences from the surrounding tissue. In mammals, the female germline is particularly precious: despite recent suggestions that germline stem cells exist in the ovary, it is still generally accepted that the ovarian reserve is finite, and its size is dependant on germ cells of the fetal ovary initiating meiosis in a timely manner. SUMMARY Prior to 2006, evidence suggested that gonadal germ cells initiate meiotic prophase I by default, but more recent data support a key role for the signalling molecule retinoic acid (RA) in instructing female germ cell fate. Newer findings also support a key meiosis-inducing role for another signalling molecule, bone morphogenic protein (BMP). Nonetheless, many questions remain. KEY MESSAGES Here, we review knowledge thus far regarding extrinsic and intrinsic determinants of a female germ cell fate, focusing on the mouse model.
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Affiliation(s)
- Cassy Spiller
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Josephine Bowles
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
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7
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Hishida T, Vazquez-Ferrer E, Hishida-Nozaki Y, Takemoto Y, Hatanaka F, Yoshida K, Prieto J, Sahu SK, Takahashi Y, Reddy P, O’Keefe DD, Rodriguez Esteban C, Knoepfler PS, Nuñez Delicado E, Castells A, Campistol JM, Kato R, Nakagawa H, Izpisua Belmonte JC. Myc Supports Self-Renewal of Basal Cells in the Esophageal Epithelium. Front Cell Dev Biol 2022; 10:786031. [PMID: 35309931 PMCID: PMC8931341 DOI: 10.3389/fcell.2022.786031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 02/04/2022] [Indexed: 11/17/2022] Open
Abstract
It is widely believed that cellular senescence plays a critical role in both aging and cancer, and that senescence is a fundamental, permanent growth arrest that somatic cells cannot avoid. Here we show that Myc plays an important role in self-renewal of esophageal epithelial cells, contributing to their resistance to cellular senescence. Myc is homogeneously expressed in basal cells of the esophageal epithelium and Myc positively regulates their self-renewal by maintaining their undifferentiated state. Indeed, Myc knockout induced a loss of the undifferentiated state of esophageal epithelial cells resulting in cellular senescence while forced MYC expression promoted oncogenic cell proliferation. A superoxide scavenger counteracted Myc knockout-induced senescence, therefore suggesting that a mitochondrial superoxide takes part in inducing senescence. Taken together, these analyses reveal extremely low levels of cellular senescence and senescence-associated phenotypes in the esophageal epithelium, as well as a critical role for Myc in self-renewal of basal cells in this organ. This provides new avenues for studying and understanding the links between stemness and resistance to cellular senescence.
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Affiliation(s)
- Tomoaki Hishida
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States
- Laboratory of Biological Chemistry, School of Pharmaceutical Sciences, Wakayama Medical University, Wakayama, Japan
| | - Eric Vazquez-Ferrer
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Yuriko Hishida-Nozaki
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Yuto Takemoto
- Department of Basic Medical Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Fumiyuki Hatanaka
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Kei Yoshida
- Department of Basic Medical Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Javier Prieto
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Sanjeeb Kumar Sahu
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Yuta Takahashi
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Pradeep Reddy
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States
| | - David D. O’Keefe
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States
| | | | - Paul S. Knoepfler
- Department of Cell Biology and Human Anatomy, University of California, Davis, Davis, CA, United States
| | | | - Antoni Castells
- Gastroenterology Department, Hospital Clinic, CIBEREHD, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Josep M. Campistol
- Gastroenterology Department, Hospital Clinic, CIBEREHD, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Ryuji Kato
- Department of Basic Medical Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Hiroshi Nakagawa
- Division of Gastroenterology, Department of Medicine, Perelman School of Medicine, Philadelphia, PA, United States
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, United States
| | - Juan Carlos Izpisua Belmonte
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, United States
- *Correspondence: Juan Carlos Izpisua Belmonte,
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8
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Pluripotency-State-Dependent Role of Dax1 in Embryonic Stem Cells Self-Renewal. Stem Cells Int 2021; 2021:5522723. [PMID: 34335791 PMCID: PMC8286181 DOI: 10.1155/2021/5522723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/18/2021] [Accepted: 06/14/2021] [Indexed: 11/24/2022] Open
Abstract
Dax1(also known as Nr0b1) is regarded as an important component of the transcription factor network in mouse embryonic stem cells (ESCs). However, the role and the molecular mechanism of Dax1 in the maintenance of different pluripotency states are poorly understood. Here, we constructed a stable Dax1 knockout (KO) cell line using the CRISPR/Cas9 system to analyze the precise function of Dax1. We reported that 2i/LIF-ESCs had significantly lower Dax1 expression than LIF/serum-ESCs. Dax1KO ES cell lines could be established in 2i/LIF and their pluripotency was confirmed. In contrast, Dax1-null ESCs could not be continuously passaged in LIF/serum due to severe differentiation and apoptosis. In LIF/serum, the activities of the Core module and Myc module were significantly reduced, while the PRC2 module was activated after Dax1KO. The expression of most proapoptotic genes and lineage-commitment genes were drastically increased, while the downregulated expression of antiapoptotic genes and many pluripotency genes was observed. Our research on the pluripotent state-dependent role of Dax1 provides clues to understand the molecular regulation mechanism at different stages of early embryonic development.
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9
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Mathsyaraja H, Catchpole J, Freie B, Eastwood E, Babaeva E, Geuenich M, Cheng PF, Ayers J, Yu M, Wu N, Moorthi S, Poudel KR, Koehne A, Grady W, Houghton AM, Berger AH, Shiio Y, MacPherson D, Eisenman RN. Loss of MGA repression mediated by an atypical polycomb complex promotes tumor progression and invasiveness. eLife 2021; 10:e64212. [PMID: 34236315 PMCID: PMC8266391 DOI: 10.7554/elife.64212] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 06/24/2021] [Indexed: 12/19/2022] Open
Abstract
MGA, a transcription factor and member of the MYC network, is mutated or deleted in a broad spectrum of malignancies. As a critical test of a tumor suppressive role, we inactivated Mga in two mouse models of non-small cell lung cancer using a CRISPR-based approach. MGA loss significantly accelerated tumor growth in both models and led to de-repression of non-canonical Polycomb ncPRC1.6 targets, including genes involved in metastasis and meiosis. Moreover, MGA deletion in human lung adenocarcinoma lines augmented invasive capabilities. We further show that MGA-MAX, E2F6, and L3MBTL2 co-occupy thousands of promoters and that MGA stabilizes these ncPRC1.6 subunits. Lastly, we report that MGA loss also induces a pro-growth effect in human colon organoids. Our studies establish MGA as a bona fide tumor suppressor in vivo and suggest a tumor suppressive mechanism in adenocarcinomas resulting from widespread transcriptional attenuation of MYC and E2F target genes mediated by MGA-MAX associated with a non-canonical Polycomb complex.
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Affiliation(s)
- Haritha Mathsyaraja
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Jonathen Catchpole
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Brian Freie
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Emily Eastwood
- Human Biology and Public Health Sciences Divisions, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Ekaterina Babaeva
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Michael Geuenich
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Pei Feng Cheng
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Jessica Ayers
- Clinical Research Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Ming Yu
- Clinical Research Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Nan Wu
- Human Biology and Public Health Sciences Divisions, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Sitapriya Moorthi
- Human Biology and Public Health Sciences Divisions, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Kumud R Poudel
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Amanda Koehne
- Comparative Pathology, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - William Grady
- Clinical Research Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
- Department of Medicine, University of Washington School of MedicineSeattleUnited States
| | - A McGarry Houghton
- Human Biology and Public Health Sciences Divisions, Fred Hutchinson Cancer Research CenterSeattleUnited States
- Clinical Research Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Alice H Berger
- Human Biology and Public Health Sciences Divisions, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Yuzuru Shiio
- Greehey Children's Cancer Research Institute, The University of Texas Health Science CenterSan AntonioUnited States
| | - David MacPherson
- Human Biology and Public Health Sciences Divisions, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Robert N Eisenman
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
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10
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Ando Y, Okeyo KO, Sunaga J, Adachi T. Edge-localized alteration in pluripotency state of mouse ES cells forming topography-confined layers on designed mesh substrates. Stem Cell Res 2021; 53:102352. [PMID: 33901814 DOI: 10.1016/j.scr.2021.102352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 03/15/2021] [Accepted: 04/09/2021] [Indexed: 10/21/2022] Open
Abstract
Self-organization of pluripotent stem cells during tissue formation is directed by the adhesion microenvironment, which defines the resulting tissue topography. Although the influence of tissue topography on pluripotency state has been inferred, this aspect of self-organization remains largely unexplored. In this study, to determine the effect of self-organized tissue topography on pluripotency loss, we designed novel island mesh substrates to confine the self-organization process of mouse embryonic stem cells, enabling us to generate isolated cell layers with an island-like topography and overhanging edges. Using immunofluorescence microscopy, we determined that cells at the tissue edge exhibited deformed nuclei associated with low OCT3/4, in contrast with cells nested in the tissue interior which had round-shaped nuclei and exhibited sustained OCT3/4 expression. Interestingly, F-actin and phospho-myosin light chain were visibly enriched at the tissue edge where ERK activation and elevated AP-2γ expression were also found to be localized, as determined using both immunofluorescence microscopy and RT-qPCR analysis. Since actomyosin contractility is known to cause ERK activation, these results suggest that mechanical condition at the tissue edge can contribute to loss of pluripotency leading to differentiation. Thus, our study draws attention to the influence of self-organized tissue topography in stem cell culture and differentiation.
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Affiliation(s)
- Yuta Ando
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Kyoto daigaku-katsura, Nishikyo-ku, Kyoto 615-8530, Japan; Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Kennedy Omondi Okeyo
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Kyoto daigaku-katsura, Nishikyo-ku, Kyoto 615-8530, Japan; Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan; Division of Systemic Life Science, Graduate School of Biostudies, Kyoto University, Yoshida-Konoecho, Sakyo-ku, Kyoto 606-8501, Japan.
| | - Junko Sunaga
- Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Taiji Adachi
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Kyoto daigaku-katsura, Nishikyo-ku, Kyoto 615-8530, Japan; Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan; Division of Systemic Life Science, Graduate School of Biostudies, Kyoto University, Yoshida-Konoecho, Sakyo-ku, Kyoto 606-8501, Japan
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11
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Qin J, Wang C, Zhu Y, Su T, Dong L, Huang Y, Hao K. Mga safeguards embryonic stem cells from acquiring extraembryonic endoderm fates. SCIENCE ADVANCES 2021; 7:7/4/eabe5689. [PMID: 33523934 PMCID: PMC7821913 DOI: 10.1126/sciadv.abe5689] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/24/2020] [Indexed: 05/17/2023]
Abstract
Polycomb group (PcG) proteins form multiprotein complexes that affect stem cell identity and fate decisions by still largely unexplored mechanisms. Here, by performing a CRISPR-based loss-of-function screen in embryonic stem cells (ESCs), we identify PcG gene Mga involved in the repression of endodermal transcription factor Gata6 We report that deletion of Mga results in peri-implantation embryonic lethality in mice. We further demonstrate that Mga-null ESCs exhibit impaired self-renewal and spontaneous differentiation to primitive endoderm (PE). Our data support a model in which Mga might serve as a scaffold for PRC1.6 assembly and guide this multimeric complex to specific genomic targets including genes that encode endodermal factors Gata4, Gata6, and Sox17. Our findings uncover an unexpected function of Mga in ESCs, where it functions as a gatekeeper to prevent ESCs from entering into the PE lineage by directly repressing expression of a set of endoderm differentiation master genes.
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Affiliation(s)
- Jinzhong Qin
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing, China.
| | - Congcong Wang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing, China
| | - Yaru Zhu
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing, China
| | - Ting Su
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing, China
| | - Lixia Dong
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing, China
| | - Yikai Huang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing, China
| | - Kunying Hao
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing, China
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12
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Hashimoto M, Sasaki H. Epiblast Formation by TEAD-YAP-Dependent Expression of Pluripotency Factors and Competitive Elimination of Unspecified Cells. Dev Cell 2019; 50:139-154.e5. [PMID: 31204175 DOI: 10.1016/j.devcel.2019.05.024] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 03/29/2019] [Accepted: 05/10/2019] [Indexed: 01/15/2023]
Abstract
The epiblast is a pluripotent cell population first formed in preimplantation embryos, and its quality is important for proper development. Here, we examined the mechanisms of epiblast formation and found that the Hippo pathway transcription factor TEAD and its coactivator YAP regulate expression of pluripotency factors. After specification of the inner cell mass, YAP accumulates in the nuclei and activates TEAD. TEAD activity is required for strong expression of pluripotency factors and is variable in the forming epiblast. Cells showing low TEAD activity are eliminated from the epiblast through cell competition. Pluripotency factor expression and MYC control cell competition downstream of TEAD activity. Cell competition eliminates unspecified cells and is required for proper organization of the epiblast. These results suggest that induction of pluripotency factors by TEAD activity and elimination of unspecified cells via cell competition ensure the production of an epiblast with naive pluripotency.
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Affiliation(s)
- Masakazu Hashimoto
- Laboratory for Embryogenesis, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hiroshi Sasaki
- Laboratory for Embryogenesis, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan.
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13
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Azami T, Matsumoto K, Jeon H, Waku T, Muratani M, Niwa H, Takahashi S, Ema M. Klf5 suppresses ERK signaling in mouse pluripotent stem cells. PLoS One 2018; 13:e0207321. [PMID: 30452437 PMCID: PMC6242311 DOI: 10.1371/journal.pone.0207321] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 10/29/2018] [Indexed: 01/05/2023] Open
Abstract
Mouse embryonic stem cells (ESCs) are pluripotent stem cells, which have the ability to differentiate into all three germ layers: mesoderm, endoderm, and ectoderm. Proper levels of phosphorylated extracellular signal-regulated kinase (pERK) are critical for maintaining pluripotency, as elevated pERK evoked by fibroblast growth factor (FGF) receptor activation results in differentiation of ESCs, while, conversely, reduction of pERK by a MEK inhibitor maintains a pluripotent ground state. However, mechanisms underlying proper control of pERK levels in mouse ESCs are not fully understood. Here, we find that Klf5, a Krüppel-like transcription factor family member, is a component of pERK regulation in mouse ESCs. We show that ERK signaling is overactivated in Klf5-KO ESCs and the overactivated ERK in Klf5-KO ESCs is suppressed by the introduction of Klf5, but not Klf2 or Klf4, indicating a unique role for Klf5 in ERK suppression. Moreover, Klf5 regulates Spred1, a negative regulator of the FGF-ERK pathway. Klf5 also facilitates reprogramming of EpiSCs into a naïve state in combination with a glycogen synthase kinase 3 inhibitor and LIF, and in place of a MEK inhibitor. Taken together, these results show for the first time that Klf5 has a unique role suppressing ERK activity in mouse ESCs.
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Affiliation(s)
- Takuya Azami
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Seta, Tsukinowa-cho, Otsu, Shiga, Japan
| | - Ken Matsumoto
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Seta, Tsukinowa-cho, Otsu, Shiga, Japan
| | - Hyojung Jeon
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Tsuyoshi Waku
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Masafumi Muratani
- Department of Genome Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hitoshi Niwa
- Department of Pluripotent Stem Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Chuo-ku, Kumamoto, Japan
| | - Satoru Takahashi
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
- International Institute for Integrative Sleep Medicine (IIIS), University of Tsukuba, Tsukuba, Ibaraki, Japan
- Life Science Center (TARA), University of Tsukuba, Tsukuba, Ibaraki, Japan
- Transborder Medical Research Center (TMRC), University of Tsukuba, Tsukuba, Ibaraki, Japan
- Laboratory Animal Resource Center (LARC), University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Masatsugu Ema
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Seta, Tsukinowa-cho, Otsu, Shiga, Japan
- PRESTO, Japan Science and Technology Agency, Saitama, Japan
- * E-mail:
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14
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Tatsumi D, Hayashi Y, Endo M, Kobayashi H, Yoshioka T, Kiso K, Kanno S, Nakai Y, Maeda I, Mochizuki K, Tachibana M, Koseki H, Okuda A, Yasui A, Kono T, Matsui Y. DNMTs and SETDB1 function as co-repressors in MAX-mediated repression of germ cell-related genes in mouse embryonic stem cells. PLoS One 2018; 13:e0205969. [PMID: 30403691 PMCID: PMC6221296 DOI: 10.1371/journal.pone.0205969] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 09/28/2018] [Indexed: 11/19/2022] Open
Abstract
In embryonic stem cells (ESCs), the expression of development-related genes, including germ cell-related genes, is globally repressed. The transcription factor MAX represses germ cell-related gene expression in ESCs via PCGF6-polycomb repressive complex 1 (PRC1), which consists of several epigenetic factors. However, we predicted that MAX represses germ cell-related gene expression through several additional mechanisms because PCGF6-PRC1 regulates the expression of only a subset of genes repressed by MAX. Here, we report that MAX associated with DNA methyltransferases (DNMTs) and the histone methyltransferase SETDB1 cooperatively control germ cell-related gene expression in ESCs. Both DNA methylation and histone H3 lysine 9 tri-methylation of the promoter regions of several germ cell-related genes were not affected by knockout of the PRC1 components, indicating that the MAX-DNMT and MAX-SETDB1 pathways are independent of the PCGF6-PRC1 pathway. Our findings provide insights into our understanding of MAX-based repressive mechanisms of germ cell-related genes in ESCs.
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Affiliation(s)
- Daiki Tatsumi
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, Miyagi, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Yohei Hayashi
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, Miyagi, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
- The Japan Agency for Medical Research and Development-Core Research for Evolutional Science and Technology (AMED-CREST), Chuo-ku, Tokyo, Japan
| | - Mai Endo
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, Miyagi, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Hisato Kobayashi
- NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Takumi Yoshioka
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Kohei Kiso
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, Miyagi, Japan
- Tohoku University School of Medicine, Sendai, Miyagi, Japan
| | - Shinichiro Kanno
- Division of Dynamic Proteome in Cancer and Aging, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi, Japan
| | - Yuji Nakai
- Institute for Food Sciences, Hirosaki University, Hirosaki, Aomori, Japan
| | - Ikuma Maeda
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, Miyagi, Japan
| | - Kentaro Mochizuki
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, Miyagi, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
- Center for Environmental Conservation and Research Safety, Tohoku University, Sendai, Miyagi, Japan
| | - Makoto Tachibana
- Department of Enzyme Chemistry, Institute for Enzyme Research, Tokushima University, Shinkura-cho, Tokushima, Japan
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- Core Research for Evolutional Science and Technology, Yokohama, Kanagawa, Japan
| | - Akihiko Okuda
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Yamane Hidaka, Saitama, Japan
| | - Akira Yasui
- Division of Dynamic Proteome in Cancer and Aging, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi, Japan
| | - Tomohiro Kono
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Yasuhisa Matsui
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, Miyagi, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
- The Japan Agency for Medical Research and Development-Core Research for Evolutional Science and Technology (AMED-CREST), Chuo-ku, Tokyo, Japan
- Center for Regulatory Epigenome and Diseases, Tohoku University School of Medicine, Sendai, Miyagi, Japan
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15
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Pérez-Olivares M, Trento A, Rodriguez-Acebes S, González-Acosta D, Fernández-Antorán D, Román-García S, Martinez D, López-Briones T, Torroja C, Carrasco YR, Méndez J, Moreno de Alborán I. Functional interplay between c-Myc and Max in B lymphocyte differentiation. EMBO Rep 2018; 19:embr.201845770. [PMID: 30126925 DOI: 10.15252/embr.201845770] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 07/26/2018] [Accepted: 07/30/2018] [Indexed: 12/11/2022] Open
Abstract
The Myc family of oncogenic transcription factors regulates myriad cellular functions. Myc proteins contain a basic region/helix-loop-helix/leucine zipper domain that mediates DNA binding and heterodimerization with its partner Max. Among the Myc proteins, c-Myc is the most widely expressed and relevant in primary B lymphocytes. There is evidence suggesting that c-Myc can perform some of its functions in the absence of Max in different cellular contexts. However, the functional in vivo interplay between c-Myc and Max during B lymphocyte differentiation is not well understood. Using in vivo and ex vivo models, we show that while c-Myc requires Max in primary B lymphocytes, several key biological processes, such as cell differentiation and DNA replication, can initially progress without the formation of c-Myc/Max heterodimers. We also describe that B lymphocytes lacking Myc, Max, or both show upregulation of signaling pathways associated with the B-cell receptor. These data suggest that c-Myc/Max heterodimers are not essential for the initiation of a subset of important biological processes in B lymphocytes, but are required for fine-tuning the initial response after activation.
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Affiliation(s)
- Mercedes Pérez-Olivares
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB)-CSIC, Madrid, Spain
| | - Alfonsina Trento
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB)-CSIC, Madrid, Spain
| | | | | | - David Fernández-Antorán
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB)-CSIC, Madrid, Spain
| | - Sara Román-García
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB)-CSIC, Madrid, Spain
| | - Dolores Martinez
- Centro Nacional de Investigaciones Oncológicas-CNIO, Madrid, Spain
| | | | - Carlos Torroja
- Centro Nacional de Investigaciones Cardiovasculares-CNIC Carlos III, Madrid, Spain
| | - Yolanda R Carrasco
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB)-CSIC, Madrid, Spain
| | - Juan Méndez
- Centro Nacional de Investigaciones Oncológicas-CNIO, Madrid, Spain
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16
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Yoshida GJ. Emerging roles of Myc in stem cell biology and novel tumor therapies. J Exp Clin Cancer Res 2018; 37:173. [PMID: 30053872 PMCID: PMC6062976 DOI: 10.1186/s13046-018-0835-y] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/06/2018] [Indexed: 02/08/2023] Open
Abstract
The pathophysiological roles and the therapeutic potentials of Myc family are reviewed in this article. The physiological functions and molecular machineries in stem cells, including embryonic stem (ES) cells and induced pluripotent stem (iPS) cells, are clearly described. The c-Myc/Max complex inhibits the ectopic differentiation of both types of artificial stem cells. Whereas c-Myc plays a fundamental role as a "double-edged sword" promoting both iPS cells generation and malignant transformation, L-Myc contributes to the nuclear reprogramming with the significant down-regulation of differentiation-associated genetic expression. Furthermore, given the therapeutic resistance of neuroendocrine tumors such as small-cell lung cancer and neuroblastoma, the roles of N-Myc in difficult-to-treat tumors are discussed. N-Myc and p53 exhibit the co-localization in the nucleus and alter p53-dependent transcriptional responses which are necessary for DNA repair, anti-apoptosis, and lipid metabolic reprogramming. NCYM protein stabilizes N-Myc, resulting in the stimulation of Oct4 expression, while Oct4 induces both N-Myc and NCYM via direct transcriptional activation of N-Myc, [corrected] thereby leading to the enhanced metastatic potential. Importantly enough, accumulating evidence strongly suggests that c-Myc can be a promising therapeutic target molecule among Myc family in terms of the biological characteristics of cancer stem-like cells (CSCs). The presence of CSCs leads to the intra-tumoral heterogeneity, which is mainly responsible for the therapeutic resistance. Mechanistically, it has been shown that Myc-induced epigenetic reprogramming enhances the CSC phenotypes. In this review article, the author describes two major therapeutic strategies of CSCs by targeting c-Myc; Firstly, Myc-dependent metabolic reprogramming is closely related to CD44 variant-dependent redox stress regulation in CSCs. It has been shown that c-Myc increases NADPH production via enhanced glutaminolysis with a finely-regulated mechanism. Secondly, the dormancy of CSCs due to FBW7-depedent c-Myc degradation pathway is also responsible for the therapeutic resistance to the conventional anti-tumor agents, the action points of which are largely dependent on the operation of the cell cycle. That is why the loss-of-functional mutations of FBW7 gene are expected to trigger "awakening" of dormant CSCs in the niche with c-Myc up-regulation. Collectively, although the further research is warranted to develop the effective anti-tumor therapeutic strategy targeting Myc family, we cancer researchers should always catch up with the current advances in the complex functions of Myc family in highly-malignant and heterogeneous tumor cells to realize the precision medicine.
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Affiliation(s)
- Go J Yoshida
- Department of Pathological Cell Biology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
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17
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Fukuda K, Okuda A, Yusa K, Shinkai Y. A CRISPR knockout screen identifies SETDB1-target retroelement silencing factors in embryonic stem cells. Genome Res 2018; 28:846-858. [PMID: 29728365 PMCID: PMC5991520 DOI: 10.1101/gr.227280.117] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 04/26/2018] [Indexed: 12/16/2022]
Abstract
In mouse embryonic stem cells (mESCs), the expression of provirus and endogenous retroelements is epigenetically repressed. Although many cellular factors involved in retroelement silencing have been identified, the complete molecular mechanism remains elusive. In this study, we performed a genome-wide CRISPR screen to advance our understanding of retroelement silencing in mESCs. The Moloney murine leukemia virus (MLV)–based retroviral vector MSCV-GFP, which is repressed by the SETDB1/TRIM28 pathway in mESCs, was used as a reporter provirus, and we identified more than 80 genes involved in this process. In particular, ATF7IP and the BAF complex components are linked with the repression of most of the SETDB1 targets. We characterized two factors, MORC2A and RESF1, of which RESF1 is a novel molecule in retroelement silencing. Although both factors are recruited to repress provirus, their roles in repression are different. MORC2A appears to function dependent on repressive epigenetic modifications, while RESF1 regulates repressive epigenetic modifications associated with SETDB1. Our genome-wide CRISPR screen cataloged genes which function at different levels in silencing of SETDB1-target retroelements and provides a useful resource for further molecular studies.
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Affiliation(s)
- Kei Fukuda
- Cellular Memory Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Akihiko Okuda
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane Hidaka Saitama 350-1241, Japan
| | - Kosuke Yusa
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Yoichi Shinkai
- Cellular Memory Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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18
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Ruan Y, He J, Wu W, He P, Tian Y, Xiao L, Liu G, Wang J, Cheng Y, Zhang S, Yang Y, Xiong J, Zhao K, Wan Y, Huang H, Zhang J, Jian R. Nac1 promotes self-renewal of embryonic stem cells through direct transcriptional regulation of c-Myc. Oncotarget 2018; 8:47607-47618. [PMID: 28548937 PMCID: PMC5564591 DOI: 10.18632/oncotarget.17744] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 04/27/2017] [Indexed: 01/11/2023] Open
Abstract
The pluripotency transcriptional network in embryonic stem cells (ESCs) is composed of distinct functional units including the core and Myc units. It is hoped that dissection of the cellular functions and interconnections of network factors will aid our understanding of ESC and cancer biology. Proteomic and genomic approaches have identified Nac1 as a member of the core pluripotency network. However, previous studies have predominantly focused on the role of Nac1 in psychomotor stimulant response and cancer pathogenesis. In this study, we report that Nac1 is a self-renewal promoting factor, but is not required for maintaining pluripotency of ESCs. Loss of function of Nac1 in ESCs results in a reduced proliferation rate and an enhanced differentiation propensity. Nac1 overexpression promotes ESC proliferation and delays ESC differentiation in the absence of leukemia inhibitory factor (LIF). Furthermore, we demonstrated that Nac1 directly binds to the c-Myc promoter and regulates c-Myc transcription. The study also revealed that the function of Nac1 in promoting ESC self-renewal appears to be partially mediated by c-Myc. These findings establish a functional link between the core and c-Myc-centered networks and provide new insights into mechanisms of stemness regulation in ESCs and cancer.
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Affiliation(s)
- Yan Ruan
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, Third Military Medical University, Chongqing 400038, China.,Biomedical Analysis Center, Third Military Medical University, Chongqing 400038, China
| | - Jianrong He
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, Third Military Medical University, Chongqing 400038, China.,Department of Anesthesiology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Wei Wu
- Department of Cardiothoracic Surgery, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Ping He
- Department of Cardiothoracic Surgery, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Yanping Tian
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, Third Military Medical University, Chongqing 400038, China
| | - Lan Xiao
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, Third Military Medical University, Chongqing 400038, China
| | - Gaoke Liu
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, Third Military Medical University, Chongqing 400038, China
| | - Jiali Wang
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, Third Military Medical University, Chongqing 400038, China
| | - Yuda Cheng
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, Third Military Medical University, Chongqing 400038, China
| | - Shuo Zhang
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, Third Military Medical University, Chongqing 400038, China
| | - Yi Yang
- Experimental Center of Basic Medicine, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | - Jiaxiang Xiong
- Experimental Center of Basic Medicine, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | - Ke Zhao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Ying Wan
- Biomedical Analysis Center, Third Military Medical University, Chongqing 400038, China
| | - He Huang
- Department of Anesthesiology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Junlei Zhang
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, Third Military Medical University, Chongqing 400038, China
| | - Rui Jian
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, Third Military Medical University, Chongqing 400038, China
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19
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Abstract
Tissue-specific transcription factors primarily act to define the phenotype of the cell. The power of a single transcription factor to alter cell fate is often minimal, as seen in gain-of-function analyses, but when multiple transcription factors cooperate synergistically it potentiates their ability to induce changes in cell fate. By contrast, transcription factor function is often dispensable in the maintenance of cell phenotype, as is evident in loss-of-function assays. Why does this phenomenon, commonly known as redundancy, occur? Here, I discuss the role that transcription factor networks play in collaboratively regulating stem cell fate and differentiation by providing multiple explanations for their functional redundancy.
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Affiliation(s)
- Hitoshi Niwa
- Department of Pluripotent Stem Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
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20
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Stielow B, Finkernagel F, Stiewe T, Nist A, Suske G. MGA, L3MBTL2 and E2F6 determine genomic binding of the non-canonical Polycomb repressive complex PRC1.6. PLoS Genet 2018; 14:e1007193. [PMID: 29381691 PMCID: PMC5806899 DOI: 10.1371/journal.pgen.1007193] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 02/09/2018] [Accepted: 01/09/2018] [Indexed: 02/02/2023] Open
Abstract
Diverse Polycomb repressive complexes 1 (PRC1) play essential roles in gene regulation, differentiation and development. Six major groups of PRC1 complexes that differ in their subunit composition have been identified in mammals. How the different PRC1 complexes are recruited to specific genomic sites is poorly understood. The Polycomb Ring finger protein PCGF6, the transcription factors MGA and E2F6, and the histone-binding protein L3MBTL2 are specific components of the non-canonical PRC1.6 complex. In this study, we have investigated their role in genomic targeting of PRC1.6. ChIP-seq analysis revealed colocalization of MGA, L3MBTL2, E2F6 and PCGF6 genome-wide. Ablation of MGA in a human cell line by CRISPR/Cas resulted in complete loss of PRC1.6 binding. Rescue experiments revealed that MGA recruits PRC1.6 to specific loci both by DNA binding-dependent and by DNA binding-independent mechanisms. Depletion of L3MBTL2 and E2F6 but not of PCGF6 resulted in differential, locus-specific loss of PRC1.6 binding illustrating that different subunits mediate PRC1.6 loading to distinct sets of promoters. Mga, L3mbtl2 and Pcgf6 colocalize also in mouse embryonic stem cells, where PRC1.6 has been linked to repression of germ cell-related genes. Our findings unveil strikingly different genomic recruitment mechanisms of the non-canonical PRC1.6 complex, which specify its cell type- and context-specific regulatory functions. Polycomb group proteins assemble in two major repressive multi-subunit complexes (PRC1 and PRC2), which play important roles in many physiological processes, including stem cell maintenance, differentiation, cell cycle control and cancer. In mammals, six different groups of PRC1 complexes exist (PRC1.1 to PRC1.6), which differ in their subunit composition. The mechanisms that target the different PRC1 complexes to specific genomic sites appear diverse and are poorly understood. In this study, we have investigated the genomic targeting mechanisms of the non-canonical PRC1.6 complex. In PRC1.6, the defining subunit PCGF6 is specifically associated with several proteins including the transcription factors MGA and E2F6, and the histone-binding protein L3MBTL2. We found that MGA is absolutely essential for targeting PRC1.6. MGA executes recruitment of PRC1.6 to its target sites through two distinct functions. On the one hand it acts as a sequence-specific DNA-binding factor; on the other hand it has a scaffolding function, which is independent of its DNA binding capacity. E2F6 and L3MBTL2 are also important in genomic targeting of PRC1.6 as they promote binding of PRC1.6 to different sets of genes associated with distinct functions. Our finding that different components specify loading of PRC1.6 to distinct sets of genes could establish a paradigm for other chromatin-associated complexes.
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Affiliation(s)
- Bastian Stielow
- Institute of Molecular Biology and Tumor Research (IMT), Philipps-University of Marburg, Marburg, Germany
| | - Florian Finkernagel
- Institute of Molecular Biology and Tumor Research (IMT), Philipps-University of Marburg, Marburg, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Center for Tumor Biology and Immunology (ZTI), Philipps-University of Marburg, Marburg, Germany
| | - Andrea Nist
- Genomics Core Facility, Center for Tumor Biology and Immunology (ZTI), Philipps-University of Marburg, Marburg, Germany
| | - Guntram Suske
- Institute of Molecular Biology and Tumor Research (IMT), Philipps-University of Marburg, Marburg, Germany
- * E-mail:
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21
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Pfeuty B, Kress C, Pain B. Network Features and Dynamical Landscape of Naive and Primed Pluripotency. Biophys J 2018; 114:237-248. [PMID: 29320691 PMCID: PMC5773751 DOI: 10.1016/j.bpj.2017.10.033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 10/02/2017] [Accepted: 10/16/2017] [Indexed: 12/31/2022] Open
Abstract
Although the broad and unique differentiation potential of pluripotent stem cells relies on a complex transcriptional network centered around Oct4, Sox2, and Nanog, two well-distinct pluripotent states, called "naive" and "primed", have been described in vitro and markedly differ in their developmental potential, their expression profiles, their signaling requirements, and their reciprocal conversion. Aiming to determine the key features that segregate and coordinate these two states, data-driven optimization of network models is performed to identify relevant parameter regimes and reduce network complexity to its core structure. Decision dynamics of optimized networks is characterized by signal-dependent multistability and strongly asymmetric transitions among naive, primed, and nonpluripotent states. Further model perturbation and reduction approaches reveal that such a dynamical landscape of pluripotency involves a functional partitioning of the regulatory network. Specifically, two overlapping positive feedback modules, Klf4/Esrrb/Nanog and Oct4/Nanog, stabilize the naive or the primed state, respectively. In turn, their incoherent feedforward and negative feedback coupling mediated by the Erk/Gsk3 module is critical for robust segregation and sequential progression between naive and primed states before irreversible exit from pluripotency.
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Affiliation(s)
- Benjamin Pfeuty
- Laboratoire de Physique des Lasers, Atomes et Molécules, Université de Lille, CNRS, Villeneuve d'Ascq, France.
| | - Clémence Kress
- Stem Cell and Brain Research Institute, Univ. Lyon, Université Claude Bernard Lyon 1, INSERM, INRA, U1208, USC1361, Bron, France
| | - Bertrand Pain
- Stem Cell and Brain Research Institute, Univ. Lyon, Université Claude Bernard Lyon 1, INSERM, INRA, U1208, USC1361, Bron, France
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22
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Endoh M, Endo TA, Shinga J, Hayashi K, Farcas A, Ma KW, Ito S, Sharif J, Endoh T, Onaga N, Nakayama M, Ishikura T, Masui O, Kessler BM, Suda T, Ohara O, Okuda A, Klose R, Koseki H. PCGF6-PRC1 suppresses premature differentiation of mouse embryonic stem cells by regulating germ cell-related genes. eLife 2017; 6:21064. [PMID: 28304275 PMCID: PMC5375644 DOI: 10.7554/elife.21064] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 03/15/2017] [Indexed: 12/22/2022] Open
Abstract
The ring finger protein PCGF6 (polycomb group ring finger 6) interacts with RING1A/B and E2F6 associated factors to form a non-canonical PRC1 (polycomb repressive complex 1) known as PCGF6-PRC1. Here, we demonstrate that PCGF6-PRC1 plays a role in repressing a subset of PRC1 target genes by recruiting RING1B and mediating downstream mono-ubiquitination of histone H2A. PCGF6-PRC1 bound loci are highly enriched for promoters of germ cell-related genes in mouse embryonic stem cells (ESCs). Conditional ablation of Pcgf6 in ESCs leads to robust de-repression of such germ cell-related genes, in turn affecting cell growth and viability. We also find a role for PCGF6 in pre- and peri-implantation mouse embryonic development. We further show that a heterodimer of the transcription factors MAX and MGA recruits PCGF6 to target loci. PCGF6 thus links sequence specific target recognition by the MAX/MGA complex to PRC1-dependent transcriptional silencing of germ cell-specific genes in pluripotent stem cells.
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Affiliation(s)
- Mitsuhiro Endoh
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Core Research for Evolutional Science and Technology, Yokohama, Japan.,Centre for Translational Medicine,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan.,Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Takaho A Endo
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Jun Shinga
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Katsuhiko Hayashi
- Department of Developmental Stem Cell Biology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Anca Farcas
- Department of Biochemistry, Oxford University, Oxford, United Kingdom
| | - Kit-Wan Ma
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shinsuke Ito
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Core Research for Evolutional Science and Technology, Yokohama, Japan
| | - Jafar Sharif
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Core Research for Evolutional Science and Technology, Yokohama, Japan
| | - Tamie Endoh
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Centre for Translational Medicine,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Naoko Onaga
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Manabu Nakayama
- Chromosome Engineering Team, Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Tomoyuki Ishikura
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Osamu Masui
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Benedikt M Kessler
- Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Toshio Suda
- Centre for Translational Medicine,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Osamu Ohara
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Chromosome Engineering Team, Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Akihiko Okuda
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan
| | - Robert Klose
- Department of Biochemistry, Oxford University, Oxford, United Kingdom
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Core Research for Evolutional Science and Technology, Yokohama, Japan
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23
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Yan Y, Yang X, Li TT, Gu KL, Hao J, Zhang Q, Wang Y. Significant differences of function and expression of microRNAs between ground state and serum-cultured pluripotent stem cells. J Genet Genomics 2017; 44:179-189. [PMID: 28411033 DOI: 10.1016/j.jgg.2017.01.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 01/16/2017] [Accepted: 01/16/2017] [Indexed: 01/08/2023]
Abstract
Serum- and 2i-cultured embryonic stem cells (ESCs) show different epigenetic landscapes and transcriptomic profiles. The difference in the function and expression of microRNAs (miRNAs) between these two states remains unclear. Here, we showed that 2i- and serum-cultured ESCs exhibited distinctive miRNA expression profiles with >100 miRNAs differentially expressed, and the expression changes were largely due to transcriptional regulation. We further characterized the function of miRNAs differentially expressed under two conditions and found that ESCs exhibited higher degree of dependency on miRNAs for rapid proliferation; since Dgcr8-/- or Dicer1-/- but not wild-type ESCs showed slower growth rate and more accumulation in the G1 phase under 2i than serum condition. More interestingly, introduction of various self-renewal-silencing miRNAs in wild-type or Dgcr8-/- ESCs failed to silence the self-renewal in 2i medium, but regained the ability to silence the self-renewal upon the addition of serum. Our findings reveal significant differences in the expression and function of miRNAs between serum- and 2i-cultured ESCs.
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Affiliation(s)
- Ying Yan
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Xi Yang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Ting-Ting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100871, China
| | - Kai-Li Gu
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Jing Hao
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Qiang Zhang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Yangming Wang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China.
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24
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Wu J, Platero-Luengo A, Sakurai M, Sugawara A, Gil MA, Yamauchi T, Suzuki K, Bogliotti YS, Cuello C, Morales Valencia M, Okumura D, Luo J, Vilariño M, Parrilla I, Soto DA, Martinez CA, Hishida T, Sánchez-Bautista S, Martinez-Martinez ML, Wang H, Nohalez A, Aizawa E, Martinez-Redondo P, Ocampo A, Reddy P, Roca J, Maga EA, Esteban CR, Berggren WT, Nuñez Delicado E, Lajara J, Guillen I, Guillen P, Campistol JM, Martinez EA, Ross PJ, Izpisua Belmonte JC. Interspecies Chimerism with Mammalian Pluripotent Stem Cells. Cell 2017; 168:473-486.e15. [PMID: 28129541 PMCID: PMC5679265 DOI: 10.1016/j.cell.2016.12.036] [Citation(s) in RCA: 326] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 10/30/2016] [Accepted: 12/22/2016] [Indexed: 01/12/2023]
Abstract
Interspecies blastocyst complementation enables organ-specific enrichment of xenogenic pluripotent stem cell (PSC) derivatives. Here, we establish a versatile blastocyst complementation platform based on CRISPR-Cas9-mediated zygote genome editing and show enrichment of rat PSC-derivatives in several tissues of gene-edited organogenesis-disabled mice. Besides gaining insights into species evolution, embryogenesis, and human disease, interspecies blastocyst complementation might allow human organ generation in animals whose organ size, anatomy, and physiology are closer to humans. To date, however, whether human PSCs (hPSCs) can contribute to chimera formation in non-rodent species remains unknown. We systematically evaluate the chimeric competency of several types of hPSCs using a more diversified clade of mammals, the ungulates. We find that naïve hPSCs robustly engraft in both pig and cattle pre-implantation blastocysts but show limited contribution to post-implantation pig embryos. Instead, an intermediate hPSC type exhibits higher degree of chimerism and is able to generate differentiated progenies in post-implantation pig embryos.
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Affiliation(s)
- Jun Wu
- Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Aida Platero-Luengo
- Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Masahiro Sakurai
- Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Atsushi Sugawara
- Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Maria Antonia Gil
- Department of Animal Medicine and Surgery, University of Murcia Campus de Espinardo, 30100 Murcia, Spain
| | - Takayoshi Yamauchi
- Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Keiichiro Suzuki
- Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Yanina Soledad Bogliotti
- Department of Animal Science, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Cristina Cuello
- Department of Animal Medicine and Surgery, University of Murcia Campus de Espinardo, 30100 Murcia, Spain
| | | | - Daiji Okumura
- Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jingping Luo
- Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Marcela Vilariño
- Department of Animal Science, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Inmaculada Parrilla
- Department of Animal Medicine and Surgery, University of Murcia Campus de Espinardo, 30100 Murcia, Spain
| | - Delia Alba Soto
- Department of Animal Science, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Cristina A Martinez
- Department of Animal Medicine and Surgery, University of Murcia Campus de Espinardo, 30100 Murcia, Spain
| | - Tomoaki Hishida
- Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sonia Sánchez-Bautista
- Universidad Católica San Antonio de Murcia (UCAM) Campus de los Jerónimos, N° 135 Guadalupe 30107 Murcia, Spain
| | - M Llanos Martinez-Martinez
- Universidad Católica San Antonio de Murcia (UCAM) Campus de los Jerónimos, N° 135 Guadalupe 30107 Murcia, Spain
| | - Huili Wang
- Department of Animal Science, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Alicia Nohalez
- Department of Animal Medicine and Surgery, University of Murcia Campus de Espinardo, 30100 Murcia, Spain
| | - Emi Aizawa
- Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | | | - Alejandro Ocampo
- Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Pradeep Reddy
- Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jordi Roca
- Department of Animal Medicine and Surgery, University of Murcia Campus de Espinardo, 30100 Murcia, Spain
| | - Elizabeth A Maga
- Department of Animal Science, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | | | - W Travis Berggren
- Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Estrella Nuñez Delicado
- Universidad Católica San Antonio de Murcia (UCAM) Campus de los Jerónimos, N° 135 Guadalupe 30107 Murcia, Spain
| | - Jeronimo Lajara
- Universidad Católica San Antonio de Murcia (UCAM) Campus de los Jerónimos, N° 135 Guadalupe 30107 Murcia, Spain
| | - Isabel Guillen
- Clinica Centro Fundación Pedro Guillén, Clínica CEMTRO, Avenida Ventisquero de la Condesa 42, 28035 Madrid, Spain
| | - Pedro Guillen
- Universidad Católica San Antonio de Murcia (UCAM) Campus de los Jerónimos, N° 135 Guadalupe 30107 Murcia, Spain; Clinica Centro Fundación Pedro Guillén, Clínica CEMTRO, Avenida Ventisquero de la Condesa 42, 28035 Madrid, Spain
| | - Josep M Campistol
- Hospital Clínico de Barcelona-IDIBAPS, Universitat de Barcelona, 08007 Barcelona, Spain
| | - Emilio A Martinez
- Department of Animal Medicine and Surgery, University of Murcia Campus de Espinardo, 30100 Murcia, Spain
| | - Pablo Juan Ross
- Department of Animal Science, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
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25
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Zhao W, Tong H, Huang Y, Yan Y, Teng H, Xia Y, Jiang Q, Qin J. Essential Role for Polycomb Group Protein Pcgf6 in Embryonic Stem Cell Maintenance and a Noncanonical Polycomb Repressive Complex 1 (PRC1) Integrity. J Biol Chem 2017; 292:2773-2784. [PMID: 28049731 DOI: 10.1074/jbc.m116.763961] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 12/29/2016] [Indexed: 11/06/2022] Open
Abstract
The Polycomb group (PcG) proteins have an important role in controlling the expression of key genes implicated in embryonic development, differentiation, and decision of cell fates. Emerging evidence suggests that Polycomb repressive complexes 1 (PRC1) is defined by the six Polycomb group RING finger protein (Pcgf) paralogs, and Pcgf proteins can assemble into noncanonical PRC1 complexes. However, little is known about the precise mechanisms of differently composed noncanonical PRC1 in the maintenance of the pluripotent cell state. Here we disrupt the Pcgf genes in mouse embryonic stem cells by CRISPR-Cas9 and find Pcgf6 null embryonic stem cells display severe defects in self-renewal and differentiation. Furthermore, Pcgf6 regulates genes mostly involved in differentiation and spermatogenesis by assembling a noncanonical PRC1 complex PRC1.6. Notably, Pcgf6 deletion causes a dramatic decrease in PRC1.6 binding to target genes and no loss of H2AK119ub1. Thus, Pcgf6 is essential for recruitment of PRC1.6 to chromatin. Our results reveal a previously uncharacterized, H2AK119ub1-independent chromatin assembly associated with PRC1.6 complex.
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Affiliation(s)
- Wukui Zhao
- From the MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, Nanjing 210061, China
| | - Huan Tong
- From the MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, Nanjing 210061, China
| | - Yikai Huang
- From the MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, Nanjing 210061, China
| | - Yun Yan
- From the MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, Nanjing 210061, China
| | - Huajian Teng
- From the MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, Nanjing 210061, China
| | - Yin Xia
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China, and
| | - Qing Jiang
- Department of Sports Medicine and Adult Reconstructive Surgery, Nanjing Drum Tower Hospital Affiliated to Medical School of Nanjing University, Nanjing 210008, China
| | - Jinzhong Qin
- From the MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, Nanjing 210061, China,
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26
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Percharde M, Bulut-Karslioglu A, Ramalho-Santos M. Hypertranscription in Development, Stem Cells, and Regeneration. Dev Cell 2016; 40:9-21. [PMID: 27989554 DOI: 10.1016/j.devcel.2016.11.010] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/23/2016] [Accepted: 11/16/2016] [Indexed: 11/29/2022]
Abstract
Cells can globally upregulate their transcriptome during specific transitions, a phenomenon called hypertranscription. Evidence for hypertranscription dates back over 70 years but has gone largely ignored in the genomics era until recently. We discuss data supporting the notion that hypertranscription is a unifying theme in embryonic development, stem cell biology, regeneration, and cell competition. We review the history, methods for analysis, underlying mechanisms, and biological significance of hypertranscription.
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Affiliation(s)
- Michelle Percharde
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Aydan Bulut-Karslioglu
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Miguel Ramalho-Santos
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA.
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27
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A Myc-driven self-reinforcing regulatory network maintains mouse embryonic stem cell identity. Nat Commun 2016; 7:11903. [PMID: 27301576 PMCID: PMC4912626 DOI: 10.1038/ncomms11903] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 05/10/2016] [Indexed: 01/09/2023] Open
Abstract
Stem cell identity depends on the integration of extrinsic and intrinsic signals, which directly influence the maintenance of their epigenetic state. Although Myc transcription factors play a major role in stem cell self-renewal and pluripotency, their integration with signalling pathways and epigenetic regulators remains poorly defined. We addressed this point by profiling the gene expression and epigenetic pattern in ESCs whose growth depends on conditional Myc activity. Here we show that Myc potentiates the Wnt/β-catenin signalling pathway, which cooperates with the transcriptional regulatory network in sustaining ESC self-renewal. Myc activation results in the transcriptional repression of Wnt antagonists through the direct recruitment of PRC2 on these targets. The consequent potentiation of the autocrine Wnt/β-catenin signalling induces the transcriptional activation of the endogenous Myc family members, which in turn activates a Myc-driven self-reinforcing circuit. Thus, our data unravel a Myc-dependent self-propagating epigenetic memory in the maintenance of ESC self-renewal capacity. The Myc transcription factor is a major regulator of stem cell (SC) self-renewal and pluripotency but how this integrates signals from other pathways is unclear. Here, the authors show that Myc activation triggers epigenetic memory in self renewing embryonic SCs via PRC2-mediated potentiation of the Wnt pathway.
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28
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Affiliation(s)
- Akihiko Okuda
- a Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University , Saitama , Japan
| | - Ayumu Suzuki
- a Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University , Saitama , Japan
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29
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Suzuki A, Hirasaki M, Hishida T, Wu J, Okamura D, Ueda A, Nishimoto M, Nakachi Y, Mizuno Y, Okazaki Y, Matsui Y, Izpisua Belmonte JC, Okuda A. Loss of MAX results in meiotic entry in mouse embryonic and germline stem cells. Nat Commun 2016; 7:11056. [PMID: 27025988 PMCID: PMC4820925 DOI: 10.1038/ncomms11056] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Accepted: 02/16/2016] [Indexed: 01/15/2023] Open
Abstract
Meiosis is a unique process that allows the generation of reproductive cells. It
remains largely unknown how meiosis is initiated in germ cells and why non-germline
cells do not undergo meiosis. We previously demonstrated that knockdown of
Max expression, a gene encoding a partner of MYC family proteins,
strongly activates expression of germ cell-related genes in ESCs. Here we find that
complete ablation of Max expression in ESCs results in profound cytological
changes reminiscent of cells undergoing meiotic cell division. Furthermore, our
analyses uncovers that Max expression is transiently attenuated in germ cells
undergoing meiosis in vivo and its forced reduction induces meiosis-like
cytological changes in cultured germline stem cells. Mechanistically, Max
depletion alterations are, in part, due to impairment of the function of an atypical
PRC1 complex (PRC1.6), in which MAX is one of the components. Our data highlight MAX
as a new regulator of meiotic onset. The mechanisms that trigger meiosis in germ cells and halt this
process in non-germline cells are unclear. Here, the authors show that knockout of
Max in embryonic stem cells results in meiotic onset in a mechanism that
involves the PRC1 complex.
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Affiliation(s)
- Ayumu Suzuki
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Yamane Hidaka, Saitama 350-1241, Japan
| | - Masataka Hirasaki
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Yamane Hidaka, Saitama 350-1241, Japan
| | - Tomoaki Hishida
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Yamane Hidaka, Saitama 350-1241, Japan.,Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Jun Wu
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Daiji Okamura
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA.,Universidad Católica San Antonio de Murcia (UCAM) Campus de los Jerónimos, No. 135, Guadalupe, 30107 Murcia, Spain
| | - Atsushi Ueda
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Yamane Hidaka, Saitama 350-1241, Japan
| | - Masazumi Nishimoto
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Yamane Hidaka, Saitama 350-1241, Japan
| | - Yutaka Nakachi
- Division of Translational Research, Research Center for Genomic Medicine, Saitama Medical University, Yamane Hidaka, Saitama 350-1241, Japan.,Division of Functional Genomics and Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Yamane Hidaka, Saitama 350-1241, Japan
| | - Yosuke Mizuno
- Division of Functional Genomics and Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Yamane Hidaka, Saitama 350-1241, Japan
| | - Yasushi Okazaki
- Division of Translational Research, Research Center for Genomic Medicine, Saitama Medical University, Yamane Hidaka, Saitama 350-1241, Japan.,Division of Functional Genomics and Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Yamane Hidaka, Saitama 350-1241, Japan
| | - Yasuhisa Matsui
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575, Japan.,Japan Agency for Medical Research and Development and Development-Core Research for Evolutionary Science and Technology (AMED-CREST), Tokyo 100-0004, Japan
| | - Juan Carlos Izpisua Belmonte
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Akihiko Okuda
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Yamane Hidaka, Saitama 350-1241, Japan
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30
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Morrison G, Scognamiglio R, Trumpp A, Smith A. Convergence of cMyc and β-catenin on Tcf7l1 enables endoderm specification. EMBO J 2016; 35:356-68. [PMID: 26675138 PMCID: PMC4741304 DOI: 10.15252/embj.201592116] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 11/03/2015] [Accepted: 11/09/2015] [Indexed: 02/02/2023] Open
Abstract
The molecular machinery that directs formation of definitive endoderm from pluripotent stem cells is not well understood. Wnt/β-catenin and Nodal signalling have been implicated, but the requirements for lineage specification remain incompletely defined. Here, we demonstrate a potent effect of inhibiting glycogen synthase kinase 3 (GSK3) on definitive endoderm production. We find that downstream of GSK3 inhibition, elevated cMyc and β-catenin act in parallel to reduce transcription and DNA binding, respectively, of the transcriptional repressor Tcf7l1. Tcf7l1 represses FoxA2, a pioneer factor for endoderm specification. Deletion of Tcf7l1 is sufficient to allow upregulation of FoxA2 in the presence of Activin. In wild-type cells, cMyc contributes by reducing Tcf7l1 mRNA, while β-catenin acts on Tcf7l1 protein. GSK3 inhibition is further required for consolidation of endodermal fate via upregulation of Sox17, highlighting sequential roles for Wnt signalling. The identification of a cMyc/β-catenin-Tcf7l1-FoxA2 axis reveals a de-repression mechanism underlying endoderm induction that may be recapitulated in other developmental and patho-logical contexts.
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Affiliation(s)
- Gillian Morrison
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Roberta Scognamiglio
- Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
| | - Andreas Trumpp
- Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
| | - Austin Smith
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK Department of Biochemistry, University of Cambridge, Cambridge, UK
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31
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Katano M, Ema M, Nakachi Y, Mizuno Y, Hirasaki M, Suzuki A, Ueda A, Nishimoto M, Takahashi S, Okazaki Y, Okuda A. Forced expression of Nanog or Esrrb preserves the ESC status in the absence of nucleostemin expression. Stem Cells 2016; 33:1089-101. [PMID: 25522312 PMCID: PMC4409032 DOI: 10.1002/stem.1918] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 11/04/2014] [Accepted: 11/21/2014] [Indexed: 12/21/2022]
Abstract
Nucleostemin (NS) is a nucleolar GTP-binding protein that is involved in a plethora of functions including ribosomal biogenesis and maintenance of telomere integrity. In addition to its expression in cancerous cells, the NS gene is expressed in stem cells including embryonic stem cells (ESCs). Previous knockdown and knockout studies have demonstrated that NS is important to preserve the self-renewality and high expression levels of pluripotency marker genes in ESCs. Here, we found that forced expression of Nanog or Esrrb, but not other pluripotency factors, resulted in the dispensability of NS expression in ESCs. However, the detrimental phenotypes of ESCs associated with ablation of NS expression were not mitigated by forced expression of Rad51 or a nucleolar localization-defective NS mutant that counteracts the damage associated with loss of NS expression in other NS-expressing cells such as neural stem/progenitor cells. Thus, our results indicate that NS participates in preservation of the viability and integrity of ESCs, which is distinct from that in other NS-expressing cells. Stem Cells2015;33:1089–1101
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Affiliation(s)
- Miyuki Katano
- Division of Developmental Biology, Saitama Medical University, Yamane, Hidaka, Saitama, Japan
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32
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Iseki H, Nakachi Y, Hishida T, Yamashita-Sugahara Y, Hirasaki M, Ueda A, Tanimoto Y, Iijima S, Sugiyama F, Yagami KI, Takahashi S, Okuda A, Okazaki Y. Combined Overexpression of JARID2, PRDM14, ESRRB, and SALL4A Dramatically Improves Efficiency and Kinetics of Reprogramming to Induced Pluripotent Stem Cells. Stem Cells 2015; 34:322-33. [DOI: 10.1002/stem.2243] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Revised: 09/17/2015] [Accepted: 09/21/2015] [Indexed: 12/28/2022]
Affiliation(s)
- Hiroyoshi Iseki
- Division of Functional Genomics and Systems Medicine; Saitama Medical University; Saitama Japan
- CREST, Japan Science and Technology Agency (JST); Saitama Japan
| | - Yutaka Nakachi
- Division of Functional Genomics and Systems Medicine; Saitama Medical University; Saitama Japan
- Division of Translational Research; Saitama Medical University; Saitama Japan
| | - Tomoaki Hishida
- CREST, Japan Science and Technology Agency (JST); Saitama Japan
- Division of Developmental Biology, Research Center for Genomic Medicine; Saitama Medical University; Saitama Japan
| | | | - Masataka Hirasaki
- Division of Developmental Biology, Research Center for Genomic Medicine; Saitama Medical University; Saitama Japan
| | - Atsushi Ueda
- Division of Developmental Biology, Research Center for Genomic Medicine; Saitama Medical University; Saitama Japan
| | - Yoko Tanimoto
- Laboratory Animal Resource Center; University of Tsukuba; Ibaraki Japan
| | - Saori Iijima
- Laboratory Animal Resource Center; University of Tsukuba; Ibaraki Japan
| | - Fumihiro Sugiyama
- Laboratory Animal Resource Center; University of Tsukuba; Ibaraki Japan
| | - Ken-Ichi Yagami
- Laboratory Animal Resource Center; University of Tsukuba; Ibaraki Japan
| | - Satoru Takahashi
- CREST, Japan Science and Technology Agency (JST); Saitama Japan
- Laboratory Animal Resource Center; University of Tsukuba; Ibaraki Japan
| | - Akihiko Okuda
- CREST, Japan Science and Technology Agency (JST); Saitama Japan
- Division of Developmental Biology, Research Center for Genomic Medicine; Saitama Medical University; Saitama Japan
| | - Yasushi Okazaki
- Division of Functional Genomics and Systems Medicine; Saitama Medical University; Saitama Japan
- CREST, Japan Science and Technology Agency (JST); Saitama Japan
- Division of Translational Research; Saitama Medical University; Saitama Japan
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33
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Crosstalk between stem cell and cell cycle machineries. Curr Opin Cell Biol 2015; 37:68-74. [PMID: 26520682 DOI: 10.1016/j.ceb.2015.10.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 09/03/2015] [Accepted: 10/06/2015] [Indexed: 12/22/2022]
Abstract
Pluripotent stem cells, defined by an unlimited self-renewal capacity and an undifferentiated state, are best typified by embryonic stem cells. These cells have a unique cell cycle compared to somatic cells as defined by a rapid progression through the cell cycle and a minimal time spent in G1. Recent reports indicate that pluripotency and cell cycle regulation are mechanistically linked. In this review, we discuss the reciprocal co-regulation of these processes, how this co-regulation may prevent differentiation, and how cellular reprogramming can re-establish the unique cell cycle regulation in induced pluripotent stem cells.
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34
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Akagi T, Kuure S, Uranishi K, Koide H, Costantini F, Yokota T. ETS-related transcription factors ETV4 and ETV5 are involved in proliferation and induction of differentiation-associated genes in embryonic stem (ES) cells. J Biol Chem 2015. [PMID: 26224636 DOI: 10.1074/jbc.m115.675595] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The pluripotency and self-renewal capacity of embryonic stem (ES) cells is regulated by several transcription factors. Here, we show that the ETS-related transcription factors Etv4 and Etv5 (Etv4/5) are specifically expressed in undifferentiated ES cells, and suppression of Oct3/4 results in down-regulation of Etv4/5. Simultaneous deletion of Etv4 and Etv5 (Etv4/5 double knock-out (dKO)) in ES cells resulted in a flat, epithelial cell-like appearance, whereas the morphology changed into compact colonies in a 2i medium (containing two inhibitors for GSK3 and MEK/ERK). Expression levels of self-renewal marker genes, including Oct3/4 and Nanog, were similar between wild-type and dKO ES cells, whereas proliferation of Etv4/5 dKO ES cells was decreased with overexpression of cyclin-dependent kinase inhibitors (p16/p19, p15, and p57). A differentiation assay revealed that the embryoid bodies derived from Etv4/5 dKO ES cells were smaller than the control, and expression of ectoderm marker genes, including Fgf5, Sox1, and Pax3, was not induced in dKO-derived embryoid bodies. Microarray analysis demonstrated that stem cell-related genes, including Tcf15, Gbx2, Lrh1, Zic3, and Baf60c, were significantly repressed in Etv4/5 dKO ES cells. The artificial expression of Etv4 and/or Etv5 in Etv4/5 dKO ES cells induced re-expression of Tcf15 and Gbx2. These results indicate that Etv4 and Etv5, potentially through regulation of Gbx2 and Tcf15, are involved in the ES cell proliferation and induction of differentiation-associated genes in ES cells.
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Affiliation(s)
- Tadayuki Akagi
- From the Department of Stem Cell Biology, Graduate School of Medical Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa 920-8640, Japan,
| | - Satu Kuure
- the Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland, and
| | - Kousuke Uranishi
- From the Department of Stem Cell Biology, Graduate School of Medical Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa 920-8640, Japan
| | - Hiroshi Koide
- From the Department of Stem Cell Biology, Graduate School of Medical Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa 920-8640, Japan
| | - Frank Costantini
- the Department of Genetics and Development, Columbia University Medical Center, New York, New York 10032
| | - Takashi Yokota
- From the Department of Stem Cell Biology, Graduate School of Medical Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa 920-8640, Japan,
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35
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Chromatin states modify network motifs contributing to cell-specific functions. Sci Rep 2015; 5:11938. [PMID: 26169043 PMCID: PMC4500950 DOI: 10.1038/srep11938] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 06/11/2015] [Indexed: 01/06/2023] Open
Abstract
Epigenetic modification can affect many important biological processes, such as cell proliferation and apoptosis. It can alter chromatin conformation and contribute to gene regulation. To investigate how chromatin states associated with network motifs, we assembled chromatin state-modified regulatory networks by combining 269 ChIP-seq data and chromatin states in four cell types. We found that many chromatin states were significantly associated with network motifs, especially for feedforward loops (FFLs). These distinct chromatin state compositions contribute to different expression levels and translational control of targets in FFLs. Strikingly, the chromatin state-modified FFLs were highly cell-specific and, to a large extent, determined cell-selective functions, such as the embryonic stem cell-specific bivalent modification-related FFL with an important role in poising developmentally important genes for expression. Besides, comparisons of chromatin state-modified FFLs between cancerous/stem and primary cell lines revealed specific type of chromatin state alterations that may act together with motif structural changes cooperatively contribute to cell-to-cell functional differences. Combination of these alterations could be helpful in prioritizing candidate genes. Together, this work highlights that a dynamic epigenetic dimension can help network motifs to control cell-specific functions.
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36
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Diolaiti D, McFerrin L, Carroll PA, Eisenman RN. Functional interactions among members of the MAX and MLX transcriptional network during oncogenesis. BIOCHIMICA ET BIOPHYSICA ACTA 2015; 1849:484-500. [PMID: 24857747 PMCID: PMC4241192 DOI: 10.1016/j.bbagrm.2014.05.016] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Revised: 04/23/2014] [Accepted: 05/14/2014] [Indexed: 01/27/2023]
Abstract
The transcription factor MYC and its related family members MYCN and MYCL have been implicated in the etiology of a wide spectrum of human cancers. Compared to other oncoproteins, such as RAS or SRC, MYC is unique because its protein coding region is rarely mutated. Instead, MYC's oncogenic properties are unleashed by regulatory mutations leading to unconstrained high levels of expression. Under both normal and pathological conditions MYC regulates multiple aspects of cellular physiology including proliferation, differentiation, apoptosis, growth and metabolism by controlling the expression of thousands of genes. How a single transcription factor exerts such broad effects remains a fascinating puzzle. Notably, MYC is part of a network of bHLHLZ proteins centered on the MYC heterodimeric partner MAX and its counterpart, the MAX-like protein MLX. This network includes MXD1-4, MNT, MGA, MONDOA and MONDOB proteins. With some exceptions, MXD proteins have been functionally linked to cell cycle arrest and differentiation, while MONDO proteins control cellular metabolism. Although the temporal expression patterns of many of these proteins can differ markedly they are frequently expressed simultaneously in the same cellular context, and potentially bind to the same, or similar DNA consensus sequence. Here we review the activities and interactions among these proteins and propose that the broad spectrum of phenotypes elicited by MYC deregulation is intimately connected to the functions and regulation of the other network members. Furthermore, we provide a meta-analysis of TCGA data suggesting that the coordinate regulation of the network is important in MYC driven tumorigenesis. This article is part of a Special Issue entitled: Myc proteins in cell biology and pathology.
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Affiliation(s)
- Daniel Diolaiti
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, USA
| | - Lisa McFerrin
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, USA
| | - Patrick A Carroll
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, USA
| | - Robert N Eisenman
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, USA.
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37
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Hishida T, Nakachi Y, Mizuno Y, Katano M, Okazaki Y, Ema M, Takahashi S, Hirasaki M, Suzuki A, Ueda A, Nishimoto M, Hishida-Nozaki Y, Vazquez-Ferrer E, Sancho-Martinez I, Carlos Izpisua Belmonte J, Okuda A. Functional Compensation Between Myc and PI3K Signaling Supports Self-Renewal of Embryonic Stem Cells. Stem Cells 2015; 33:713-25. [DOI: 10.1002/stem.1893] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 09/25/2014] [Accepted: 10/15/2014] [Indexed: 11/05/2022]
Affiliation(s)
- Tomoaki Hishida
- Division of Developmental Biology; Research Center for Genomic Medicine, Saitama Medical University; Yamane Hidaka Saitama Japan
- Core Research for Evolutional Science and Technology (CREST); Japan Science and Technology Agency; Kawaguchi Saitama Japan
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla California USA
| | - Yutaka Nakachi
- Division of Translational Research; Research Center for Genomic Medicine, Saitama Medical University; Yamane Hidaka Saitama Japan
- Division of Functional Genomics and Systems Medicine; Research Center for Genomic Medicine, Saitama Medical University; Yamane Hidaka Saitama Japan
| | - Yosuke Mizuno
- Division of Functional Genomics and Systems Medicine; Research Center for Genomic Medicine, Saitama Medical University; Yamane Hidaka Saitama Japan
| | - Miyuki Katano
- Division of Developmental Biology; Research Center for Genomic Medicine, Saitama Medical University; Yamane Hidaka Saitama Japan
| | - Yasushi Okazaki
- Core Research for Evolutional Science and Technology (CREST); Japan Science and Technology Agency; Kawaguchi Saitama Japan
- Division of Translational Research; Research Center for Genomic Medicine, Saitama Medical University; Yamane Hidaka Saitama Japan
- Division of Functional Genomics and Systems Medicine; Research Center for Genomic Medicine, Saitama Medical University; Yamane Hidaka Saitama Japan
| | - Masatsugu Ema
- Department of Anatomy and Embryology; Institute of Basic Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba; Tsukuba Japan
| | - Satoru Takahashi
- Core Research for Evolutional Science and Technology (CREST); Japan Science and Technology Agency; Kawaguchi Saitama Japan
- Department of Anatomy and Embryology; Institute of Basic Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba; Tsukuba Japan
| | - Masataka Hirasaki
- Division of Developmental Biology; Research Center for Genomic Medicine, Saitama Medical University; Yamane Hidaka Saitama Japan
| | - Ayumu Suzuki
- Division of Developmental Biology; Research Center for Genomic Medicine, Saitama Medical University; Yamane Hidaka Saitama Japan
| | - Atsushi Ueda
- Division of Developmental Biology; Research Center for Genomic Medicine, Saitama Medical University; Yamane Hidaka Saitama Japan
| | - Masazumi Nishimoto
- Radioisotope Experimental Laboratory; Research Center for Genomic Medicine, Saitama Medical University; Yamane Hidaka Saitama Japan
| | - Yuriko Hishida-Nozaki
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla California USA
| | - Eric Vazquez-Ferrer
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla California USA
| | | | | | - Akihiko Okuda
- Division of Developmental Biology; Research Center for Genomic Medicine, Saitama Medical University; Yamane Hidaka Saitama Japan
- Core Research for Evolutional Science and Technology (CREST); Japan Science and Technology Agency; Kawaguchi Saitama Japan
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38
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Fujimoto M, Ohte S, Shin M, Yoneyama K, Osawa K, Miyamoto A, Tsukamoto S, Mizuta T, Kokabu S, Machiya A, Okuda A, Suda N, Katagiri T. Establishment of a novel model of chondrogenesis using murine embryonic stem cells carrying fibrodysplasia ossificans progressiva-associated mutant ALK2. Biochem Biophys Res Commun 2014; 455:347-52. [PMID: 25446088 DOI: 10.1016/j.bbrc.2014.11.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 11/07/2014] [Indexed: 01/05/2023]
Abstract
Fibrodysplasia ossificans progressiva (FOP) is a genetic disorder characterized by heterotopic endochondral ossification in soft tissue. A mutation in the bone morphogenetic protein (BMP) receptor ALK2, R206H, has been identified in patients with typical FOP. In the present study, we established murine embryonic stem (ES) cells that express wild-type human ALK2 or typical mutant human ALK2 [ALK2(R206H)] under the control of the Tet-Off system. Although wild-type ALK2 and mutant ALK2(R206H) were expressed in response to a withdrawal of doxycycline (Dox), BMP signaling was activated only in the mutant ALK2(R206H)-expressing cells without the addition of exogenous BMPs. The Dox-dependent induction of BMP signaling was blocked by a specific kinase inhibitor of the BMP receptor. The mutant ALK2(R206H)-carrying cells showed Dox-regulated chondrogenesis in vitro, which occurred in co-operation with transforming growth factor-β1 (TGF-β1). Overall, our ES cells are useful for studying the molecular mechanisms of heterotopic ossification in FOP in vitro and for developing novel inhibitors of chondrogenesis induced by mutant ALK2(R206H) associated with FOP.
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Affiliation(s)
- Mai Fujimoto
- Division of Pathophysiology, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka-shi, Saitama 350-1241, Japan; Division of Orthodontics, Department of Human Development and Fostering, Meikai University School of Dentistry, 1-1 Keyakidai, Sakado-shi, Saitama 350-0283, Japan
| | - Satoshi Ohte
- Division of Pathophysiology, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka-shi, Saitama 350-1241, Japan
| | - Masashi Shin
- Division of Pathophysiology, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka-shi, Saitama 350-1241, Japan
| | - Katsumi Yoneyama
- Division of Pathophysiology, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka-shi, Saitama 350-1241, Japan
| | - Kenji Osawa
- Division of Pathophysiology, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka-shi, Saitama 350-1241, Japan
| | - Arei Miyamoto
- Division of Pathophysiology, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka-shi, Saitama 350-1241, Japan
| | - Sho Tsukamoto
- Division of Pathophysiology, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka-shi, Saitama 350-1241, Japan
| | - Takato Mizuta
- Division of Pathophysiology, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka-shi, Saitama 350-1241, Japan
| | - Shoichiro Kokabu
- Division of Pathophysiology, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka-shi, Saitama 350-1241, Japan
| | - Aiko Machiya
- Division of Pathophysiology, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka-shi, Saitama 350-1241, Japan; Division of Orthodontics, Department of Human Development and Fostering, Meikai University School of Dentistry, 1-1 Keyakidai, Sakado-shi, Saitama 350-0283, Japan
| | - Akihiko Okuda
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka-shi, Saitama 350-1241, Japan
| | - Naoto Suda
- Division of Orthodontics, Department of Human Development and Fostering, Meikai University School of Dentistry, 1-1 Keyakidai, Sakado-shi, Saitama 350-0283, Japan
| | - Takenobu Katagiri
- Division of Pathophysiology, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka-shi, Saitama 350-1241, Japan.
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39
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Mateo JL, van den Berg DLC, Haeussler M, Drechsel D, Gaber ZB, Castro DS, Robson P, Lu QR, Crawford GE, Flicek P, Ettwiller L, Wittbrodt J, Guillemot F, Martynoga B. Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal. Genome Res 2014; 25:41-56. [PMID: 25294244 PMCID: PMC4317172 DOI: 10.1101/gr.173435.114] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The gene regulatory network (GRN) that supports neural stem cell (NS cell) self-renewal has so far been poorly characterized. Knowledge of the central transcription factors (TFs), the noncoding gene regulatory regions that they bind to, and the genes whose expression they modulate will be crucial in unlocking the full therapeutic potential of these cells. Here, we use DNase-seq in combination with analysis of histone modifications to identify multiple classes of epigenetically and functionally distinct cis-regulatory elements (CREs). Through motif analysis and ChIP-seq, we identify several of the crucial TF regulators of NS cells. At the core of the network are TFs of the basic helix-loop-helix (bHLH), nuclear factor I (NFI), SOX, and FOX families, with CREs often densely bound by several of these different TFs. We use machine learning to highlight several crucial regulatory features of the network that underpin NS cell self-renewal and multipotency. We validate our predictions by functional analysis of the bHLH TF OLIG2. This TF makes an important contribution to NS cell self-renewal by concurrently activating pro-proliferation genes and preventing the untimely activation of genes promoting neuronal differentiation and stem cell quiescence.
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Affiliation(s)
- Juan L Mateo
- Centre for Organismal Studies (COS) Heidelberg, University of Heidelberg, 69120 Heidelberg, Germany;
| | - Debbie L C van den Berg
- Division of Molecular Neurobiology, MRC-National Institute for Medical Research, Mill Hill, London NW7 1AA, United Kingdom
| | - Maximilian Haeussler
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Daniela Drechsel
- Division of Molecular Neurobiology, MRC-National Institute for Medical Research, Mill Hill, London NW7 1AA, United Kingdom
| | - Zachary B Gaber
- Division of Molecular Neurobiology, MRC-National Institute for Medical Research, Mill Hill, London NW7 1AA, United Kingdom
| | - Diogo S Castro
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Paul Robson
- Developmental Cellomics Laboratory, Genome Institute of Singapore, Singapore 138672, Singapore
| | | | - Gregory E Crawford
- Institute of Genome Sciences and Policy, Duke University, Durham, North Carolina 27708, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Laurence Ettwiller
- Centre for Organismal Studies (COS) Heidelberg, University of Heidelberg, 69120 Heidelberg, Germany; New England Biolabs, Inc., Ipswich, Massachusetts 01938-2723, USA
| | - Joachim Wittbrodt
- Centre for Organismal Studies (COS) Heidelberg, University of Heidelberg, 69120 Heidelberg, Germany
| | - François Guillemot
- Division of Molecular Neurobiology, MRC-National Institute for Medical Research, Mill Hill, London NW7 1AA, United Kingdom
| | - Ben Martynoga
- Division of Molecular Neurobiology, MRC-National Institute for Medical Research, Mill Hill, London NW7 1AA, United Kingdom;
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Transcription regulation and chromatin structure in the pluripotent ground state. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:129-37. [DOI: 10.1016/j.bbagrm.2013.09.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 09/06/2013] [Accepted: 09/07/2013] [Indexed: 01/19/2023]
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Myc and max genome-wide binding sites analysis links the Myc regulatory network with the polycomb and the core pluripotency networks in mouse embryonic stem cells. PLoS One 2014; 9:e88933. [PMID: 24586446 PMCID: PMC3931652 DOI: 10.1371/journal.pone.0088933] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 01/14/2014] [Indexed: 12/20/2022] Open
Abstract
Myc is a master transcription factor that has been demonstrated to be required for embryonic stem cell (ESC) pluripotency, self-renewal, and inhibition of differentiation. Although recent works have identified several Myc-targets in ESCs, the list of Myc binding sites is largely incomplete due to the low sensitivity and specificity of the antibodies available. To systematically identify Myc binding sites in mouse ESCs, we used a stringent streptavidin-based genome-wide chromatin immunoprecipitation (ChIP-Seq) approach with biotin-tagged Myc (Bio-Myc) as well as a ChIP-Seq of the Myc binding partner Max. This analysis identified 4325 Myc binding sites, of which 2885 were newly identified. The identified sites overlap with more than 85% of the Max binding sites and are enriched for H3K4me3-positive promoters and active enhancers. Remarkably, this analysis unveils that Myc/Max regulates chromatin modifiers and transcriptional regulators involved in stem cell self-renewal linking the Myc-centered network with the Polycomb and the Core networks. These results provide insights into the contribution of Myc and Max in maintaining stem cell self-renewal and keeping these cells in an undifferentiated state.
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42
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Gastaldi C, Bertero T, Xu N, Bourget-Ponzio I, Lebrigand K, Fourre S, Popa A, Cardot-Leccia N, Meneguzzi G, Sonkoly E, Pivarcsi A, Mari B, Barbry P, Ponzio G, Rezzonico R. miR-193b/365a cluster controls progression of epidermal squamous cell carcinoma. Carcinogenesis 2013; 35:1110-20. [PMID: 24374827 DOI: 10.1093/carcin/bgt490] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Incidence of cutaneous squamous cell carcinomas (cSCCs) constantly increases in the Caucasian population. Developing preferentially on precancerous lesions such as actinic keratoses due to chronic sunlight exposure, cSCCs result from the malignant transformation of keratinocytes. Although a resection of the primary tumor is usually curative, a subset of aggressive cSCCs shows a high risk of recurrence and metastases. The characterization of the molecular dysfunctions involved in cSCC development should help to identify new relevant targets against these aggressive cSCCs. In that context, we have used small RNA sequencing to identify 100 microRNAs (miRNAs) whose expression was altered during chemically induced mouse skin tumorigenesis. The decreased expression of the miR-193b/365a cluster during tumor progression suggests a tumor suppressor role. Ectopic expression of these miRNAs in tumor cells indeed inhibited their proliferation, clonogenic potential and migration, which were stimulated in normal keratinocytes when these miRNAs were blocked with antisense oligonucleotides. A combination of in silico predictions and transcriptome analyses identified several target genes of interest. We validated KRAS and MAX as direct targets of miR-193b and miR-365a. Repression of these targets using siRNAs mimicked the effects of miR-193b and miR-365a, suggesting that these genes might mediate, at least in part, the tumor-suppressive action of these miRNAs.
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Affiliation(s)
- Cécile Gastaldi
- UMR 7275, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, 660 route des Lucioles, F-06560 Valbonne, France
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43
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Hirasaki M, Hiraki-Kamon K, Kamon M, Suzuki A, Katano M, Nishimoto M, Okuda A. Striking similarity in the gene expression levels of individual Myc module members among ESCs, EpiSCs, and partial iPSCs. PLoS One 2013; 8:e83769. [PMID: 24386274 PMCID: PMC3873369 DOI: 10.1371/journal.pone.0083769] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 11/08/2013] [Indexed: 02/05/2023] Open
Abstract
Predominant transcriptional subnetworks called Core, Myc, and PRC modules have been shown to participate in preservation of the pluripotency and self-renewality of embryonic stem cells (ESCs). Epiblast stem cells (EpiSCs) are another cell type that possesses pluripotency and self-renewality. However, the roles of these modules in EpiSCs have not been systematically examined to date. Here, we compared the average expression levels of Core, Myc, and PRC module genes between ESCs and EpiSCs. EpiSCs showed substantially higher and lower expression levels of PRC and Core module genes, respectively, compared with those in ESCs, while Myc module members showed almost equivalent levels of average gene expression. Subsequent analyses revealed that the similarity in gene expression levels of the Myc module between these two cell types was not just overall, but striking similarities were evident even when comparing the expression of individual genes. We also observed equivalent levels of similarity in the expression of individual Myc module genes between induced pluripotent stem cells (iPSCs) and partial iPSCs that are an unwanted byproduct generated during iPSC induction. Moreover, our data demonstrate that partial iPSCs depend on a high level of c-Myc expression for their self-renewal properties.
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Affiliation(s)
- Masataka Hirasaki
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama, Japan
| | - Keiko Hiraki-Kamon
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama, Japan
| | - Masayoshi Kamon
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama, Japan
| | - Ayumu Suzuki
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama, Japan
| | - Miyuki Katano
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama, Japan
| | - Masazumi Nishimoto
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama, Japan
| | - Akihiko Okuda
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- * E-mail:
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44
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Roles for MYC in the establishment and maintenance of pluripotency. Cold Spring Harb Perspect Med 2013; 3:a014381. [PMID: 24296349 DOI: 10.1101/cshperspect.a014381] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
MYC and MYCN have been directly implicated in the transcriptional regulation of several thousand genes in pluripotent stem cells and possibly contribute to the activity of all transcribed genes. Control of transcription by a pause-release mechanism, recruitment of positive and negative epigenetic regulators, and a general role in transcriptional amplification have all been implicated as part of the broad, overarching mechanism by which MYC controls stem cell biology. As would be anticipated from the regulation of so many genes, MYC is involved in a wide range of cellular processes including cell-cycle control, metabolism, signal transduction, self-renewal, maintenance of pluripotency, and control of cell fate decisions. MYC transcription factors also have clear roles in cell reprogramming and establishment of the pluripotent state. The mechanism by which MYC accomplishes this is now being explored and promises to uncover unexpected facets of general MYC regulation that are likely to be applicable to cancer biology. In this work we review our current understanding of how MYC contributes to the maintenance and establishment of pluripotent cells and how it contributes to early embryonic development.
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45
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Greve TS, Judson RL, Blelloch R. microRNA control of mouse and human pluripotent stem cell behavior. Annu Rev Cell Dev Biol 2013; 29:213-239. [PMID: 23875649 DOI: 10.1146/annurev-cellbio-101512-122343] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In the past decade, significant progress has been made in understanding both microRNA function and cellular pluripotency. Here we review the intersection of these two exciting fields. While microRNAs are not required for the establishment and maintenance of pluripotency in early development and cell culture, respectively, they are critically important in the regulation of the cell cycle structure of pluripotent stem cells as well as the silencing of the pluripotency program upon differentiation. Pluripotent cells, both in vivo and in vitro, dominantly express a single family of microRNAs, which can promote the reprogramming of a somatic cell back to a pluripotent state. Here, we review the known mechanisms by which these and other microRNAs regulate the different aspects of the pluripotent stem cell program in both mouse and human.
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Affiliation(s)
- Tobias S Greve
- Department of Urology and The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, Program in Biomedical Sciences, University of California, San Francisco, California, 94143
| | - Robert L Judson
- Department of Urology and The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, Program in Biomedical Sciences, University of California, San Francisco, California, 94143
| | - Robert Blelloch
- Department of Urology and The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, Program in Biomedical Sciences, University of California, San Francisco, California, 94143
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Chappell J, Sun Y, Singh A, Dalton S. MYC/MAX control ERK signaling and pluripotency by regulation of dual-specificity phosphatases 2 and 7. Genes Dev 2013; 27:725-33. [PMID: 23592794 DOI: 10.1101/gad.211300.112] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Suppression of extracellular signal-regulated kinase (ERK) signaling is an absolute requirement for the maintenance of murine pluripotent stem cells (mPSCs) and requires the MYC-binding partner MAX. In this study, we define a mechanism for this by showing that MYC/MAX complexes suppress ERK activity by transcriptionally regulating two members of the dual-specificity phosphatase (DUSP) family. DUSPs function by binding and then inactivating ERK1,2 by dephosphorylating residues required for catalytic activity. MYC/MAX complexes achieve this by binding the promoters of DUSP2 and DUSP7, leading to their transcriptional activation, resulting in the attenuation of ERK activity. In the absence of MYC, ectopic DUSP2,7 expression severely delays differentiation, while loss of DUSP2,7 ectopically activates ERK, resulting in loss of pluripotency. These findings elucidate a novel regulatory role for MYC in PSC maintenance involving the stimulation of phosphatases that directly inhibit the MAPK/ERK signaling pathway. Moreover, it provides a mechanism for how leukemia inhibitory factor (LIF)/STAT3 signaling reaches across to the MAPK/ERK pathway through MYC and MAX to sustain pluripotency.
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Affiliation(s)
- James Chappell
- Department of Biochemistry and Molecular Biology, Paul D. Coverdell Center for Biomedical and Health Sciences, The University of Georgia, Athens, Georgia 30602, USA
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47
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Max is a repressor of germ cell-related gene expression in mouse embryonic stem cells. Nat Commun 2013; 4:1754. [DOI: 10.1038/ncomms2780] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 03/20/2013] [Indexed: 12/23/2022] Open
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48
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Hishida T, Nozaki Y, Nakachi Y, Mizuno Y, Iseki H, Katano M, Kamon M, Hirasaki M, Nishimoto M, Okazaki Y, Okuda A. Sirt1, p53, and p38(MAPK) are crucial regulators of detrimental phenotypes of embryonic stem cells with Max expression ablation. Stem Cells 2013; 30:1634-44. [PMID: 22696478 DOI: 10.1002/stem.1147] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
c-Myc participates in diverse cellular processes including cell cycle control, tumorigenic transformation, and reprogramming of somatic cells to induced pluripotent cells. c-Myc is also an important regulator of self-renewal and pluripotency of embryonic stem cells (ESCs). We recently demonstrated that loss of the Max gene, encoding the best characterized partner for all Myc family proteins, causes loss of the pluripotent state and extensive cell death in ESCs strictly in this order. However, the mechanisms and molecules that are responsible for these phenotypes remain largely obscure. Here, we show that Sirt1, p53, and p38(MAPK) are crucially involved in the detrimental phenotype of Max-null ESCs. Moreover, our analyses revealed that these proteins are involved at varying levels to one another in the hierarchy of the pathway leading to cell death in Max-null ESCs.
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Affiliation(s)
- Tomoaki Hishida
- Division of Developmental Biology, Saitama Medical University, Hidaka, Saitama, Japan
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49
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Xu Y, Wei X, Wang M, Zhang R, Fu Y, Xing M, Hua Q, Xie X. Proliferation rate of somatic cells affects reprogramming efficiency. J Biol Chem 2013; 288:9767-9778. [PMID: 23439651 PMCID: PMC3617278 DOI: 10.1074/jbc.m112.403881] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The discovery of induced pluripotent stem (iPS) cells provides not only new approaches for cell replacement therapy, but also new ways for drug screening. However, the undefined mechanism and relatively low efficiency of reprogramming have limited the application of iPS cells. In an attempt to further optimize the reprogramming condition, we unexpectedly observed that removing c-Myc from the Oct-4, Sox-2, Klf-4, and c-Myc (OSKM) combination greatly enhanced the generation of iPS cells. The iPS cells generated without c-Myc attained salient pluripotent characteristics and were capable of producing full-term mice through tetraploid complementation. We observed that forced expression of c-Myc induced the expression of many genes involved in cell cycle control and a hyperproliferation state of the mouse embryonic fibroblasts during the early stage of reprogramming. This enhanced proliferation of mouse embryonic fibroblasts correlated negatively to the overall reprogramming efficiency. By applying small molecule inhibitors of cell proliferation at the early stage of reprogramming, we were able to improve the efficiency of iPS cell generation mediated by OSKM. Our data demonstrated that the proliferation rate of the somatic cell plays critical roles in reprogramming. Slowing down the proliferation of the original cells might be beneficial to the induction of iPS cells.
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Affiliation(s)
- Yongyu Xu
- Laboratory of Receptor-based Bio-medicine, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092; National Center for Drug Screening, Stake Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiaoyuan Wei
- Laboratory of Receptor-based Bio-medicine, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092; National Center for Drug Screening, Stake Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Min Wang
- National Center for Drug Screening, Stake Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Ru Zhang
- Laboratory of Receptor-based Bio-medicine, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092.
| | - Yanbin Fu
- Laboratory of Receptor-based Bio-medicine, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092; National Center for Drug Screening, Stake Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Mingzhe Xing
- Laboratory of Receptor-based Bio-medicine, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092; National Center for Drug Screening, Stake Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Qiuhong Hua
- Laboratory of Receptor-based Bio-medicine, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092
| | - Xin Xie
- Laboratory of Receptor-based Bio-medicine, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092; National Center for Drug Screening, Stake Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
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50
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Singh AM, Bechard M, Smith K, Dalton S. Reconciling the different roles of Gsk3β in "naïve" and "primed" pluripotent stem cells. Cell Cycle 2012; 11:2991-6. [PMID: 22825252 DOI: 10.4161/cc.21110] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Signaling pathways orchestrated by PI3K/Akt, Raf/Mek/Erk and Wnt/β-catenin are known to play key roles in the self-renewal and differentiation of pluripotent stem cells. The serine/threonine protein kinase Gsk3β has roles in all three pathways, making its exact function difficult to decipher. Consequently, conflicting reports have implicated Gsk3β in promoting self-renewal, while others suggest that it performs roles in the activation of differentiation pathways. Different thresholds of Gsk3β activity also have different biological effects on pluripotent cells, making this situation even more complex. Here, we describe a further level of complexity that is most apparent when comparing "naïve" murine and "primed" human pluripotent stem cells. In naïve cells, Gsk3β activity is restrained by PI3K/Akt, but when released from inhibitory signals it antagonizes self-renewal pathways by targeting pluripotency factors such as Myc and Nanog. This situation also applies in primed cells, but, in addition, a separate pool of Gsk3β is required to suppress canonical Wnt signaling. These observations suggest that different Gsk3β-protein complexes shift the balance between naïve and primed pluripotent cells and identify fundamental differences in their cell signaling. Altogether, these findings have important implications for the mechanisms underpinning the establishment of different pluripotent cell states and for the control of self-renewal and differentiation.
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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, Athens, GA, USA
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