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Liu Y, Zhang Y, Chang X, Liu X. MDIC3: Matrix decomposition to infer cell-cell communication. PATTERNS (NEW YORK, N.Y.) 2024; 5:100911. [PMID: 38370122 PMCID: PMC10873161 DOI: 10.1016/j.patter.2023.100911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 05/31/2023] [Accepted: 12/08/2023] [Indexed: 02/20/2024]
Abstract
Crosstalk among cells is vital for maintaining the biological function and intactness of systems. Most existing methods for investigating cell-cell communications are based on ligand-receptor (L-R) expression, and they focus on the study between two cells. Thus, the final communication inference results are particularly sensitive to the completeness and accuracy of the prior biological knowledge. Because existing L-R research focuses mainly on humans, most existing methods can only examine cell-cell communication for humans. As far as we know, there is currently no effective method to overcome this species limitation. Here, we propose MDIC3 (matrix decomposition to infer cell-cell communication), an unsupervised tool to investigate cell-cell communication in any species, and the results are not limited by specific L-R pairs or signaling pathways. By comparing it with existing methods for the inference of cell-cell communication, MDIC3 obtained better performance in both humans and mice.
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Affiliation(s)
- Yi Liu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- School of Mathematics and Statistics, Shandong University, Weihai 364209, China
| | - Yuelei Zhang
- School of Mathematics and Statistics, Shandong University, Weihai 364209, China
| | - Xiao Chang
- Institute of Statistics and Applied Mathematics, Anhui University of Finance and Economics, Bengbu 233030, China
| | - Xiaoping Liu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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2
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Selvarajah K, Tan JJ, Shaharuddin B. Corneal Epithelial Development and the Role of Induced Pluripotent Stem Cells for Regeneration. Curr Stem Cell Res Ther 2024; 19:292-306. [PMID: 36915985 DOI: 10.2174/1574888x18666230313094121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 12/02/2022] [Accepted: 01/02/2023] [Indexed: 03/16/2023]
Abstract
Severe corneal disorders due to infective aetiologies, trauma, chemical injuries, and chronic cicatricial inflammations, are among vision-threatening pathologies leading to permanent corneal scarring. The whole cornea or lamellar corneal transplantation is often used as a last resort to restore vision. However, limited autologous tissue sources and potential adverse post-allotransplantation sequalae urge the need for more robust and strategic alternatives. Contemporary management using cultivated corneal epithelial transplantation has paved the way for utilizing stem cells as a regenerative potential. Humaninduced pluripotent stem cells (hiPSCs) can generate ectodermal progenitors and potentially be used for ocular surface regeneration. This review summarizes the process of corneal morphogenesis and the signaling pathways underlying the development of corneal epithelium, which is key to translating the maturation and differentiation process of hiPSCs in vitro. The current state of knowledge and methodology for driving efficient corneal epithelial cell differentiation from pluripotent stem cells are highlighted.
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Affiliation(s)
- Komathi Selvarajah
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
- Department of Microbiology, Faculty of Medicine, Asian Institute of Medical Sciences and Technology (AIMST) University, Kedah, Malaysia
| | - Jun Jie Tan
- Department of Microbiology, Faculty of Medicine, Asian Institute of Medical Sciences and Technology (AIMST) University, Kedah, Malaysia
| | - Bakiah Shaharuddin
- Department of Microbiology, Faculty of Medicine, Asian Institute of Medical Sciences and Technology (AIMST) University, Kedah, Malaysia
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3
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Valcourt JR, Huang RE, Kundu S, Venkatasubramanian D, Kingston RE, Ramanathan S. Modulating mesendoderm competence during human germ layer differentiation. Cell Rep 2021; 37:109990. [PMID: 34758327 PMCID: PMC8601596 DOI: 10.1016/j.celrep.2021.109990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 08/16/2021] [Accepted: 10/21/2021] [Indexed: 12/26/2022] Open
Abstract
As pluripotent human embryonic stem cells progress toward one germ layer fate, they lose the ability to adopt alternative fates. Using a low-dimensional reaction coordinate to monitor progression toward ectoderm, we show that a differentiating stem cell's probability of adopting a mesendodermal fate given appropriate signals falls sharply at a point along the ectoderm trajectory. We use this reaction coordinate to prospectively isolate and profile differentiating cells based on their mesendoderm competence and analyze their RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin using sequencing (ATAC-seq) profiles to identify transcription factors that control the cell's mesendoderm competence. By modulating these key transcription factors, we can expand or contract the window of competence to adopt the mesendodermal fate along the ectodermal differentiation trajectory. The ability of the underlying gene regulatory network to modulate competence is essential for understanding human development and controlling the fate choices of stem cells in vitro.
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Affiliation(s)
- James R Valcourt
- Systems, Synthetic, and Quantitative Biology Program, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Division of Applied Physics, Harvard University, Cambridge, MA 02138, USA.
| | - Roya E Huang
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Division of Applied Physics, Harvard University, Cambridge, MA 02138, USA
| | - Sharmistha Kundu
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Divya Venkatasubramanian
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Division of Applied Physics, Harvard University, Cambridge, MA 02138, USA
| | - Robert E Kingston
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sharad Ramanathan
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Division of Applied Physics, Harvard University, Cambridge, MA 02138, USA; School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
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4
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Human neural tube morphogenesis in vitro by geometric constraints. Nature 2021; 599:268-272. [PMID: 34707290 PMCID: PMC8828633 DOI: 10.1038/s41586-021-04026-9] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 09/13/2021] [Indexed: 01/21/2023]
Abstract
Understanding human organ formation is a scientific challenge with far-reaching medical implications1,2. Three-dimensional stem-cell cultures have provided insights into human cell differentiation3,4. However, current approaches use scaffold-free stem-cell aggregates, which develop non-reproducible tissue shapes and variable cell-fate patterns. This limits their capacity to recapitulate organ formation. Here we present a chip-based culture system that enables self-organization of micropatterned stem cells into precise three-dimensional cell-fate patterns and organ shapes. We use this system to recreate neural tube folding from human stem cells in a dish. Upon neural induction5,6, neural ectoderm folds into a millimetre-long neural tube covered with non-neural ectoderm. Folding occurs at 90% fidelity, and anatomically resembles the developing human neural tube. We find that neural and non-neural ectoderm are necessary and sufficient for folding morphogenesis. We identify two mechanisms drive folding: (1) apical contraction of neural ectoderm, and (2) basal adhesion mediated via extracellular matrix synthesis by non-neural ectoderm. Targeting these two mechanisms using drugs leads to morphological defects similar to neural tube defects. Finally, we show that neural tissue width determines neural tube shape, suggesting that morphology along the anterior-posterior axis depends on neural ectoderm geometry in addition to molecular gradients7. Our approach provides a new route to the study of human organ morphogenesis in health and disease.
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5
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Miao X, Niibe K, Zhang M, Liu Z, Nattasit P, Ohori-Morita Y, Nakamura T, Jiang X, Egusa H. Stage-Specific Role of Amelx Activation in Stepwise Ameloblast Induction from Mouse Induced Pluripotent Stem Cells. Int J Mol Sci 2021; 22:ijms22137195. [PMID: 34281250 PMCID: PMC8268366 DOI: 10.3390/ijms22137195] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/27/2021] [Accepted: 06/27/2021] [Indexed: 01/29/2023] Open
Abstract
Amelogenin comprises ~90% of enamel proteins; however, the involvement of Amelx transcriptional activation in regulating ameloblast differentiation from induced pluripotent stem cells (iPSCs) remains unknown. In this study, we generated doxycycline-inducible Amelx-expressing mouse iPSCs (Amelx-iPSCs). We then established a three-stage ameloblast induction strategy from Amelx-iPSCs, including induction of surface ectoderm (stage 1), dental epithelial cells (DECs; stage 2), and ameloblast lineage (stage 3) in sequence, by manipulating several signaling molecules. We found that adjunctive use of lithium chloride (LiCl) in addition to bone morphogenetic protein 4 and retinoic acid promoted concentration-dependent differentiation of DECs. The resulting cells had a cobblestone appearance and keratin14 positivity. Attenuation of LiCl at stage 3 together with transforming growth factor β1 and epidermal growth factor resulted in an ameloblast lineage with elongated cell morphology, positivity for ameloblast markers, and calcium deposition. Although stage-specific activation of Amelx did not produce noticeable phenotypic changes in ameloblast differentiation, Amelx activation at stage 3 significantly enhanced cell adhesion as well as decreased proliferation and migration. These results suggest that the combination of inducible Amelx transcription and stage-specific ameloblast induction for iPSCs represents a powerful tool to highlight underlying mechanisms in ameloblast differentiation and function in association with Amelx expression.
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Affiliation(s)
- Xinchao Miao
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Miyagi, Japan; (X.M.); (M.Z.); (Z.L.); (P.N.); (Y.O.-M.)
| | - Kunimichi Niibe
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Miyagi, Japan; (X.M.); (M.Z.); (Z.L.); (P.N.); (Y.O.-M.)
- Correspondence: (K.N.); (H.E.); Tel.: +81-22-717-8363 (K.N.); +81-22-717-8363 (H.E.)
| | - Maolin Zhang
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Miyagi, Japan; (X.M.); (M.Z.); (Z.L.); (P.N.); (Y.O.-M.)
- Department of Prosthodontics, Shanghai Engineering Research Center of Advanced Dental Technology and Materials, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China;
| | - Zeni Liu
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Miyagi, Japan; (X.M.); (M.Z.); (Z.L.); (P.N.); (Y.O.-M.)
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan 430079, China
| | - Praphawi Nattasit
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Miyagi, Japan; (X.M.); (M.Z.); (Z.L.); (P.N.); (Y.O.-M.)
| | - Yumi Ohori-Morita
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Miyagi, Japan; (X.M.); (M.Z.); (Z.L.); (P.N.); (Y.O.-M.)
| | - Takashi Nakamura
- Division of Molecular Pharmacology and Cell Biophysics, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Miyagi, Japan;
| | - Xinquan Jiang
- Department of Prosthodontics, Shanghai Engineering Research Center of Advanced Dental Technology and Materials, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China;
| | - Hiroshi Egusa
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Miyagi, Japan; (X.M.); (M.Z.); (Z.L.); (P.N.); (Y.O.-M.)
- Center for Advanced Stem Cell and Regenerative Research, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Miyagi, Japan
- Correspondence: (K.N.); (H.E.); Tel.: +81-22-717-8363 (K.N.); +81-22-717-8363 (H.E.)
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6
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Hong M, Christ A, Christa A, Willnow TE, Krauss RS. Cdon mutation and fetal alcohol converge on Nodal signaling in a mouse model of holoprosencephaly. eLife 2020; 9:60351. [PMID: 32876567 PMCID: PMC7467722 DOI: 10.7554/elife.60351] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/10/2020] [Indexed: 02/07/2023] Open
Abstract
Holoprosencephaly (HPE), a defect in midline patterning of the forebrain and midface, arises ~1 in 250 conceptions. It is associated with predisposing mutations in the Nodal and Hedgehog (HH) pathways, with penetrance and expressivity graded by genetic and environmental modifiers, via poorly understood mechanisms. CDON is a multifunctional co-receptor, including for the HH pathway. In mice, Cdon mutation synergizes with fetal alcohol exposure, producing HPE phenotypes closely resembling those seen in humans. We report here that, unexpectedly, Nodal signaling is a major point of synergistic interaction between Cdon mutation and fetal alcohol. Window-of-sensitivity, genetic, and in vitro findings are consistent with a model whereby brief exposure of Cdon mutant embryos to ethanol during gastrulation transiently and partially inhibits Nodal pathway activity, with consequent effects on midline patterning. These results illuminate mechanisms of gene-environment interaction in a multifactorial model of a common birth defect.
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Affiliation(s)
- Mingi Hong
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Annabel Christ
- Max-Delbruck-Center for Molecular Medicine, Berlin, Germany
| | - Anna Christa
- Max-Delbruck-Center for Molecular Medicine, Berlin, Germany
| | | | - Robert S Krauss
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, United States
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7
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Zhong H, Ren Z, Wang X, Miao K, Ni W, Meng Y, Lu L, Wang C, Liu W, Deng CX, Xu RH, Chen G. Stagewise keratinocyte differentiation from human embryonic stem cells by defined signal transduction modulators. Int J Biol Sci 2020; 16:1450-1462. [PMID: 32210732 PMCID: PMC7085224 DOI: 10.7150/ijbs.44414] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 02/02/2020] [Indexed: 01/02/2023] Open
Abstract
Keratinocyte is the predominant cell type in the epidermis of skin, and it provides the protective barrier function for the body. Various signaling pathways have been implicated in keratinocyte differentiation in animal models; However, their temporal regulation and interactions are still to be explored in pluripotent stem cell models. In this report, we use human embryonic stem cells to demonstrate that epidermal ectoderm and subsequent keratinocyte cell fate can be determined step by step under the regulation of defined factors. The inhibition of TGFβ initiates ectodermal lineage differentiation, and the activation of BMP pathway drives epidermal TP63 expression. Meanwhile, the timely activation of WNT pathway suppresses extraembryonic lineage, and promotes epidermal cell fate. With further specification by NOTCH inhibition, more than 90% of cells become TP63-positive stage Ⅱ keratinocytes. Finally, stage Ⅲ keratinocytes are produced under defined hypo-calcium keratinocyte culture conditions, and are further matured in mouse xenograft model. This study not only establishes an in vitro platform to study keratinocyte cell fate determination, but also provides an efficient protocol to produce keratinocytes for disease models and clinical applications.
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Affiliation(s)
- Hui Zhong
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau
| | - Zhili Ren
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau
| | - Xiaoyan Wang
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau
| | - Kai Miao
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau
| | - Wenjun Ni
- Department of Urology Surgery, Zhuhai People's Hospital, Jinan University, Zhuhai, Guangdong 519000, China
| | - Ya Meng
- Zhuhai Precision Medical Center, Zhuhai People's Hospital, Jinan University, Zhuhai, Guangdong 519000, China
| | - Ligong Lu
- Zhuhai Precision Medical Center, Zhuhai People's Hospital, Jinan University, Zhuhai, Guangdong 519000, China.,Center of Interventional radiology, Zhuhai People's Hospital, Jinan University, Zhuhai, Guangdong 519000, China
| | - Chunming Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau
| | - Weiwei Liu
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau.,Bioimaging and Stem Cell Core Facility, Faculty of Health Sciences, University of Macau, Taipa, Macau
| | - Chu-Xia Deng
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau
| | - Ren-He Xu
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau
| | - Guokai Chen
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau.,Bioimaging and Stem Cell Core Facility, Faculty of Health Sciences, University of Macau, Taipa, Macau
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8
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Kuo HH, Gao X, DeKeyser JM, Fetterman KA, Pinheiro EA, Weddle CJ, Fonoudi H, Orman MV, Romero-Tejeda M, Jouni M, Blancard M, Magdy T, Epting CL, George AL, Burridge PW. Negligible-Cost and Weekend-Free Chemically Defined Human iPSC Culture. Stem Cell Reports 2020; 14:256-270. [PMID: 31928950 PMCID: PMC7013200 DOI: 10.1016/j.stemcr.2019.12.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 12/05/2019] [Accepted: 12/09/2019] [Indexed: 12/19/2022] Open
Abstract
Human induced pluripotent stem cell (hiPSC) culture has become routine, yet the cost of pluripotent cell media, frequent medium changes, and the reproducibility of differentiation have remained restrictive. Here, we describe the formulation of a hiPSC culture medium (B8) as a result of the exhaustive optimization of medium constituents and concentrations, establishing the necessity and relative contributions of each component to the pluripotent state and cell proliferation. The reagents in B8 represent only 3% of the costs of commercial media, made possible primarily by the in-lab generation of three E. coli-expressed, codon-optimized recombinant proteins: fibroblast growth factor 2, transforming growth factor β3, and neuregulin 1. We demonstrate the derivation and culture of 34 hiPSC lines in B8 as well as the maintenance of pluripotency long term (over 100 passages). This formula also allows a weekend-free feeding schedule without sacrificing capacity for differentiation.
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Affiliation(s)
- Hui-Hsuan Kuo
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Xiaozhi Gao
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jean-Marc DeKeyser
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - K Ashley Fetterman
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Emily A Pinheiro
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Carly J Weddle
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Hananeh Fonoudi
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Michael V Orman
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Marisol Romero-Tejeda
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Mariam Jouni
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Malorie Blancard
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Tarek Magdy
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Conrad L Epting
- Departments of Pediatrics and Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Alfred L George
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Paul W Burridge
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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9
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Repression of Inappropriate Gene Expression in the Vertebrate Embryonic Ectoderm. Genes (Basel) 2019; 10:genes10110895. [PMID: 31698780 PMCID: PMC6895975 DOI: 10.3390/genes10110895] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/28/2019] [Accepted: 11/04/2019] [Indexed: 01/01/2023] Open
Abstract
During vertebrate embryogenesis, precise regulation of gene expression is crucial for proper cell fate determination. Much of what we know about vertebrate development has been gleaned from experiments performed on embryos of the amphibian Xenopus laevis; this review will focus primarily on studies of this model organism. An early critical step during vertebrate development is the formation of the three primary germ layers—ectoderm, mesoderm, and endoderm—which emerge during the process of gastrulation. While much attention has been focused on the induction of mesoderm and endoderm, it has become clear that differentiation of the ectoderm involves more than the simple absence of inductive cues; rather, it additionally requires the inhibition of mesendoderm-promoting genes. This review aims to summarize our current understanding of the various inhibitors of inappropriate gene expression in the presumptive ectoderm.
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10
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Britton G, Heemskerk I, Hodge R, Qutub AA, Warmflash A. A novel self-organizing embryonic stem cell system reveals signaling logic underlying the patterning of human ectoderm. Development 2019; 146:dev.179093. [PMID: 31519692 DOI: 10.1242/dev.179093] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 09/06/2019] [Indexed: 12/20/2022]
Abstract
During development, the ectoderm is patterned by a combination of BMP and WNT signaling. Research in model organisms has provided substantial insight into this process; however, there are currently no systems in which to study ectodermal patterning in humans. Further, the complexity of neural plate border specification has made it difficult to transition from discovering the genes involved to deeper mechanistic understanding. Here, we develop an in vitro model of human ectodermal patterning, in which human embryonic stem cells self-organize to form robust and quantitatively reproducible patterns corresponding to the complete medial-lateral axis of the embryonic ectoderm. Using this platform, we show that the duration of endogenous WNT signaling is a crucial control parameter, and that cells sense relative levels of BMP and WNT signaling in making fate decisions. These insights allowed us to develop an improved protocol for placodal differentiation. Thus, our platform is a powerful tool for studying human ectoderm patterning and for improving directed differentiation protocols.This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- George Britton
- Systems Synthetic and Physical Biology Program, Rice University Houston, Houston, TX 77005, USA
| | - Idse Heemskerk
- Department of Biosciences, Rice University Houston, Houston, TX 77005, USA
| | - Rachel Hodge
- Department of Biosciences, Rice University Houston, Houston, TX 77005, USA
| | - Amina A Qutub
- Department of Bioengineering, Rice University Houston, Houston, TX 77005, USA
| | - Aryeh Warmflash
- Department of Biosciences, Rice University Houston, Houston, TX 77005, USA .,Department of Bioengineering, Rice University Houston, Houston, TX 77005, USA
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11
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Suppressing Nodal Signaling Activity Predisposes Ectodermal Differentiation of Epiblast Stem Cells. Stem Cell Reports 2018; 11:43-57. [PMID: 30008328 PMCID: PMC6067151 DOI: 10.1016/j.stemcr.2018.05.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 05/27/2018] [Accepted: 05/28/2018] [Indexed: 01/18/2023] Open
Abstract
The molecular mechanism underpinning the specification of the ectoderm, a transient germ-layer tissue, during mouse gastrulation was examined here in a stem cell-based model. We captured a self-renewing cell population with enhanced ectoderm potency from mouse epiblast stem cells (EpiSCs) by suppressing Nodal signaling activity. The transcriptome of the Nodal-inhibited EpiSCs resembles that of the anterior epiblast of embryonic day (E)7.0 and E7.5 mouse embryo, which is accompanied by chromatin modifications that reflect the priming of ectoderm lineage-related genes for expression. Nodal-inhibited EpiSCs show enhanced ectoderm differentiation in vitro and contribute to the neuroectoderm and the surface ectoderm in postimplantation chimeras but lose the propensity for mesendoderm differentiation in vitro and in chimeras. Our findings show that specification of the ectoderm progenitors is enhanced by the repression of Nodal signaling activity, and the ectoderm-like stem cells provide an experimental model to investigate the molecular characters of the epiblast-derived ectoderm. Self-renewing epiblast stem cells can be maintained under Nodal inhibition Nodal-inhibited epiblast stem cells and the ectoderm display similar transcriptome Blocking Nodal changes the epigenome to that associated with ectoderm potency Nodal-inhibited epiblast stem cells differentiate preferentially to ectodermal cells
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12
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Liu C, Peng G, Jing N. TGF-β signaling pathway in early mouse development and embryonic stem cells. Acta Biochim Biophys Sin (Shanghai) 2018; 50:68-73. [PMID: 29190317 DOI: 10.1093/abbs/gmx120] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 10/31/2017] [Indexed: 12/30/2022] Open
Abstract
TGF-β superfamily signaling pathways essentially contribute to the broad spectrum of early developmental events including embryonic patterning, cell fate determination and dynamic movements. In this review, we first introduced some key developmental processes that require TGF-β signaling to show the fundamental importance of these pathways. Then we discuss how their activities are regulated, and new findings about how the TGF-β superfamily ligands bind to the chromatin to regulate transcription during embryo development.
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Affiliation(s)
- Chang Liu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Guangdun Peng
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Naihe Jing
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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13
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Kamarudin TA, Bojic S, Collin J, Yu M, Alharthi S, Buck H, Shortt A, Armstrong L, Figueiredo FC, Lako M. Differences in the Activity of Endogenous Bone Morphogenetic Protein Signaling Impact on the Ability of Induced Pluripotent Stem Cells to Differentiate to Corneal Epithelial-Like Cells. Stem Cells 2017; 36:337-348. [PMID: 29226476 PMCID: PMC5839253 DOI: 10.1002/stem.2750] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 10/27/2017] [Accepted: 11/15/2017] [Indexed: 12/13/2022]
Abstract
Cornea is a clear outermost layer of the eye which enables transmission of light onto the retina. The transparent corneal epithelium is regenerated by limbal stem cells (LSCs), whose loss/dysfunction results in LSCs deficiency (LSCD). Ex vivo expansion of autologous LSCs obtained from patient's healthy eye followed by transplantation onto the LSCs damaged/deficient eye, has provided a successful treatment for unilateral LSCD. However, this is not applicable to patient with total bilateral LSCD, where LSCs are lost/damaged from both eyes. We investigated the potential of human induced pluripotent stem cell (hiPSC) to differentiate into corneal epithelial‐like cells as a source of autologous stem cell treatment for patients with total bilateral LSCD. Our study showed that combined addition of bone morphogenetic protein 4 (BMP4), all trans‐retinoic acid and epidermal growth factor for the first 9 days of differentiation followed by cell‐replating on collagen‐IV‐coated surfaces with a corneal‐specific‐epithelial cell media for an additional 11 days, resulted in step wise differentiation of human embryonic stem cells (hESC) to corneal epithelial progenitors and mature corneal epithelial‐like cells. We observed differences in the ability of hiPSC lines to undergo differentiation to corneal epithelial‐like cells which were dependent on the level of endogenous BMP signaling and could be restored via the activation of this signaling pathway by a specific transforming growth factor β inhibitor (SB431542). Together our data reveal a differential ability of hiPSC lines to generate corneal epithelial cells which is underlined by the activity of endogenous BMP signaling pathway. Stem Cells2018;36:337–348
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Affiliation(s)
- Taty Anna Kamarudin
- Institute of Genetic Medicine, International Centre for Life, Newcastle University, Central Parkway, Newcastle upon Tyne, United Kingdom
| | - Sanja Bojic
- Institute of Genetic Medicine, International Centre for Life, Newcastle University, Central Parkway, Newcastle upon Tyne, United Kingdom
| | - Joseph Collin
- Institute of Genetic Medicine, International Centre for Life, Newcastle University, Central Parkway, Newcastle upon Tyne, United Kingdom
| | - Min Yu
- Institute of Genetic Medicine, International Centre for Life, Newcastle University, Central Parkway, Newcastle upon Tyne, United Kingdom
| | - Sameer Alharthi
- Princess Al Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Saudi Arabia
| | - Harley Buck
- UCL Institute of Immunology and Transplantation, Royal Free Campus, London, United Kingdom
| | - Alex Shortt
- UCL Institute of Immunology and Transplantation, Royal Free Campus, London, United Kingdom
| | - Lyle Armstrong
- Institute of Genetic Medicine, International Centre for Life, Newcastle University, Central Parkway, Newcastle upon Tyne, United Kingdom
| | - Francisco C Figueiredo
- Institute of Genetic Medicine, International Centre for Life, Newcastle University, Central Parkway, Newcastle upon Tyne, United Kingdom.,Department of Ophthalmology, Royal Victoria Infirmary, Queen Victoria Road, Newcastle upon Tyne, United Kingdom
| | - Majlinda Lako
- Institute of Genetic Medicine, International Centre for Life, Newcastle University, Central Parkway, Newcastle upon Tyne, United Kingdom
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14
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Matsuda K, Mikami T, Oki S, Iida H, Andrabi M, Boss JM, Yamaguchi K, Shigenobu S, Kondoh H. ChIP-seq analysis of genomic binding regions of five major transcription factors highlights a central role for ZIC2 in the mouse epiblast stem cell gene regulatory network. Development 2017; 144:1948-1958. [PMID: 28455373 PMCID: PMC5482983 DOI: 10.1242/dev.143479] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 04/18/2017] [Indexed: 12/21/2022]
Abstract
To obtain insight into the transcription factor (TF)-dependent regulation of epiblast stem cells (EpiSCs), we performed ChIP-seq analysis of the genomic binding regions of five major TFs. Analysis of in vivo biotinylated ZIC2, OTX2, SOX2, POU5F1 and POU3F1 binding in EpiSCs identified several new features. (1) Megabase-scale genomic domains rich in ZIC2 peaks and genes alternate with those rich in POU3F1 but sparse in genes, reflecting the clustering of regulatory regions that act at short and long-range, which involve binding of ZIC2 and POU3F1, respectively. (2) The enhancers bound by ZIC2 and OTX2 prominently regulate TF genes in EpiSCs. (3) The binding sites for SOX2 and POU5F1 in mouse embryonic stem cells (ESCs) and EpiSCs are divergent, reflecting the shift in the major acting TFs from SOX2/POU5F1 in ESCs to OTX2/ZIC2 in EpiSCs. (4) This shift in the major acting TFs appears to be primed by binding of ZIC2 in ESCs at relevant genomic positions that later function as enhancers following the disengagement of SOX2/POU5F1 from major regulatory functions and subsequent binding by OTX2. These new insights into EpiSC gene regulatory networks gained from this study are highly relevant to early stage embryogenesis.
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Affiliation(s)
- Kazunari Matsuda
- Graduate School of Frontier Biosciences, Osaka University, Yamadaoka 1-3, Suita, Osaka 565-0871, Japan
| | - Tomoyuki Mikami
- Graduate School of Frontier Biosciences, Osaka University, Yamadaoka 1-3, Suita, Osaka 565-0871, Japan
| | - Shinya Oki
- Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Hideaki Iida
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-ku, Kyoto 603-8555, Japan
| | - Munazah Andrabi
- Graduate School of Frontier Biosciences, Osaka University, Yamadaoka 1-3, Suita, Osaka 565-0871, Japan
| | - Jeremy M Boss
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Katsushi Yamaguchi
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Shuji Shigenobu
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Hisato Kondoh
- Graduate School of Frontier Biosciences, Osaka University, Yamadaoka 1-3, Suita, Osaka 565-0871, Japan .,Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-ku, Kyoto 603-8555, Japan
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15
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Sherman JH, Karpinski BA, Fralish MS, Cappuzzo JM, Dhindsa DS, Thal AG, Moody SA, LaMantia AS, Maynard TM. Foxd4 is essential for establishing neural cell fate and for neuronal differentiation. Genesis 2017; 55. [PMID: 28316121 DOI: 10.1002/dvg.23031] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 03/10/2017] [Accepted: 03/13/2017] [Indexed: 01/21/2023]
Abstract
Many molecular factors required for later stages of neuronal differentiation have been identified; however, much less is known about the early events that regulate the initial establishment of the neuroectoderm. We have used an in vitro embryonic stem cell (ESC) differentiation model to investigate early events of neuronal differentiation and to define the role of mouse Foxd4, an ortholog of a forkhead-family transcription factor central to Xenopus neural plate/neuroectodermal precursor development. We found that Foxd4 is a necessary regulator of the transition from pluripotent ESC to neuroectodermal stem cell, and its expression is necessary for neuronal differentiation. Mouse Foxd4 expression is not only limited to the neural plate but it is also expressed and apparently functions to regulate neurogenesis in the olfactory placode. These in vitro results suggest that mouse Foxd4 has a similar function to its Xenopus ortholog; this was confirmed by successfully substituting murine Foxd4 for its amphibian counterpart in overexpression experiments. Thus, Foxd4 appears to regulate the initial steps in establishing neuroectodermal precursors during initial development of the nervous system.
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Affiliation(s)
- Jonathan H Sherman
- Department of Neurological Surgery, George Washington University Hospital, Washington, District of Columbia.,Institute for Neuroscience, George Washington University, Washington, District of Columbia
| | - Beverly A Karpinski
- Institute for Neuroscience, George Washington University, Washington, District of Columbia.,Department of Pharmacology and Physiology, George Washington University SMHS, Washington, District of Columbia
| | - Matthew S Fralish
- Institute for Neuroscience, George Washington University, Washington, District of Columbia.,Department of Pharmacology and Physiology, George Washington University SMHS, Washington, District of Columbia
| | | | | | - Arielle G Thal
- George Washington University SMHS, Washington, District of Columbia
| | - Sally A Moody
- Institute for Neuroscience, George Washington University, Washington, District of Columbia.,Department of Anatomy and Regenerative Biology, George Washington University SMHS, Washington, District of Columbia
| | - Anthony S LaMantia
- Institute for Neuroscience, George Washington University, Washington, District of Columbia.,Department of Pharmacology and Physiology, George Washington University SMHS, Washington, District of Columbia
| | - Thomas M Maynard
- Institute for Neuroscience, George Washington University, Washington, District of Columbia.,Department of Pharmacology and Physiology, George Washington University SMHS, Washington, District of Columbia
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16
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Jang S, Choubey S, Furchtgott L, Zou LN, Doyle A, Menon V, Loew EB, Krostag AR, Martinez RA, Madisen L, Levi BP, Ramanathan S. Dynamics of embryonic stem cell differentiation inferred from single-cell transcriptomics show a series of transitions through discrete cell states. eLife 2017; 6:20487. [PMID: 28296635 PMCID: PMC5352225 DOI: 10.7554/elife.20487] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/31/2017] [Indexed: 02/06/2023] Open
Abstract
The complexity of gene regulatory networks that lead multipotent cells to acquire different cell fates makes a quantitative understanding of differentiation challenging. Using a statistical framework to analyze single-cell transcriptomics data, we infer the gene expression dynamics of early mouse embryonic stem (mES) cell differentiation, uncovering discrete transitions across nine cell states. We validate the predicted transitions across discrete states using flow cytometry. Moreover, using live-cell microscopy, we show that individual cells undergo abrupt transitions from a naïve to primed pluripotent state. Using the inferred discrete cell states to build a probabilistic model for the underlying gene regulatory network, we further predict and experimentally verify that these states have unique response to perturbations, thus defining them functionally. Our study provides a framework to infer the dynamics of differentiation from single cell transcriptomics data and to build predictive models of the gene regulatory networks that drive the sequence of cell fate decisions during development. DOI:http://dx.doi.org/10.7554/eLife.20487.001
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Affiliation(s)
- Sumin Jang
- FAS Center for Systems Biology, Harvard University, Cambridge, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Sandeep Choubey
- FAS Center for Systems Biology, Harvard University, Cambridge, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Leon Furchtgott
- FAS Center for Systems Biology, Harvard University, Cambridge, United States.,Biophysics Program, Harvard University, Cambridge, United States
| | - Ling-Nan Zou
- FAS Center for Systems Biology, Harvard University, Cambridge, United States
| | - Adele Doyle
- FAS Center for Systems Biology, Harvard University, Cambridge, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Vilas Menon
- Allen Institute for Brain Science, Seattle, United States
| | - Ethan B Loew
- FAS Center for Systems Biology, Harvard University, Cambridge, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | | | | | - Linda Madisen
- Allen Institute for Brain Science, Seattle, United States
| | - Boaz P Levi
- Allen Institute for Brain Science, Seattle, United States
| | - Sharad Ramanathan
- FAS Center for Systems Biology, Harvard University, Cambridge, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States.,Allen Institute for Brain Science, Seattle, United States.,School of Engineering and Applied Sciences, Harvard University, Cambridge, United States.,Harvard Stem Cell Institute, Harvard University, Cambridge, United States
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17
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Peng G, Jing N. The genome-wide molecular regulation of mouse gastrulation embryo. SCIENCE CHINA-LIFE SCIENCES 2017; 60:363-369. [PMID: 28251461 DOI: 10.1007/s11427-016-0285-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 11/25/2016] [Indexed: 11/24/2022]
Abstract
The diverse morphologies among vertebrate species stems from the evolution of a basic body plan that is constituted by a spatially organized ensemble of tissue lineage progenitors. At gastrulation, this body plan is established through a coordinated morphogenetic process and the delineation of tissue lineages that are driven by the activity of the genome. To explore the molecular mechanisms, in a comprehensive context, it is imperative to glean an understanding of the region- and population-specific genetic activity underpinning this fundamental developmental process. In this review, we outline the recent progresses and the future directions in studies of genome activity for the regulation of mouse embryogenesis at gastrulation.
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Affiliation(s)
- Guangdun Peng
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Naihe Jing
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
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18
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Song L, Chen J, Peng G, Tang K, Jing N. Dynamic Heterogeneity of Brachyury in Mouse Epiblast Stem Cells Mediates Distinct Response to Extrinsic Bone Morphogenetic Protein (BMP) Signaling. J Biol Chem 2016; 291:15212-25. [PMID: 27226536 DOI: 10.1074/jbc.m115.705418] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Indexed: 01/11/2023] Open
Abstract
Mouse pluripotent cells, such as embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs), provide excellent in vitro systems to study imperative pre- and postimplantation events of in vivo mammalian development. It is known that mouse ESCs are dynamic heterogeneous populations. However, it remains largely unclear whether and how EpiSCs possess heterogeneity and plasticity similar to that of ESCs. Here, we show that EpiSCs are discriminated by the expression of a specific marker T (Brachyury) into two populations. The T-positive (T(+)) and the T-negative (T(-)) populations can be interconverted within the same culture condition. In addition, the two populations display distinct responses to bone morphogenetic protein (BMP) signaling and different developmental potentials. The T(-) EpiSCs are preferentially differentiated into ectoderm lineages, whereas T(+) EpiSCs have a biased potential for mesendoderm fates. Mechanistic studies reveal that T(+) EpiSCs have an earlier and faster response to BMP4 stimulation than T(-) EpiSCs. Id1 mediates the commitment of T(-) EpiSCs to epidermal lineage during BMP4 treatment. On the other hand, Snail modulates the conversion of T(+) EpiSCs to mesendoderm fates with the presence of BMP4. Furthermore, T expression is essential for epithelial-mesenchymal transition during EpiSCs differentiation. Our findings suggest that the dynamic heterogeneity of the T(+)/T(-) subpopulation primes EpiSCs toward particular cell lineages, providing important insights into the dynamic development of the early mouse embryo.
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Affiliation(s)
- Lu Song
- From the State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China and
| | - Jun Chen
- From the State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China and
| | - Guangdun Peng
- From the State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China and
| | - Ke Tang
- the Institute of Life Science, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Naihe Jing
- From the State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China and
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19
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Qiao Y, Yang X, Jing N. Epigenetic regulation of early neural fate commitment. Cell Mol Life Sci 2016; 73:1399-411. [PMID: 26801220 PMCID: PMC11108527 DOI: 10.1007/s00018-015-2125-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/01/2015] [Accepted: 12/22/2015] [Indexed: 12/18/2022]
Abstract
Early neural fate commitment is a key process in neural development and establishment of the central nervous system, and this process is tightly controlled by extrinsic signals, intrinsic factors, and epigenetic regulation. Here, we summarize the main findings regarding the regulatory network of epigenetic mechanisms that play important roles during early neural fate determination and embryonic development, including histone modifications, chromatin remodeling, DNA modifications, and RNA-level regulation. These regulatory mechanisms coordinate to play essential roles in silencing of pluripotency genes and activating key neurodevelopmental genes during cell fate commitment at DNA, histone, chromatin, and RNA levels. Moreover, we discuss the relationship between epigenetic regulation, signaling pathways, and intrinsic factors during early neural fate specification.
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Affiliation(s)
- Yunbo Qiao
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Xianfa Yang
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai, 200031, China
| | - Naihe Jing
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China.
- School of Life Science and Technology, Shanghai Tech University, Shanghai, 200031, China.
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